When the mechanical components check out, it's time to look closely at the commands being issued. It begins with an understanding of how the PCM uses the EGR valve.

Many technicians feel pretty comfortable diagnosing fuel control problems in modern computer-controlled automobiles, but exhaust gas recirculation (EGR) is another story. They may be comfortable testing individual EGR system components, but it can be difficult to determine 
if the powertrain control module (PCM) is controlling EGR properly. If the computer is providing any EGR commands at all, it's easy to assume they're appropriate. But this isn't always true. In fact, inappropriate EGR commands are more common than faulty air/fuel mixture commands.

Most service information is limited to testing individual components and passages, and verifying that the PCM is capable of opening the EGR valve. A vehicle can pass all of these tests and still have too much or too little EGR because of improper PCM commands. These bad commands are usually based on sensors that have drifted. Until the sensor drift causes a significant shift in fuel commands, no fault codes are set. Because of this, there are a significant number of driveability problems that OBD II fails to identify, and most of them involve improper EGR and/or ignition timing commands. 

It's about the sensors
Thanks to oxygen sensors, fuel control has very effective closed-loop feedback to keep it within appropriate limits. Some EGR systems also have limited feedback, but they can't actually determine if the EGR flow will control oxides of nitrogen (NOX) without causing driveability problems. Minor manifold absolute pressure (MAP), mass air flow (MAF), intake air temperature (IAT) and barometric pressure (BARO) faults can cause the PCM to command the wrong amount of EGR flow. When this happens, the EGR feedback system will fail to identify a problem because the EGR flow still matches the EGR command.

The DPFE sensor measures pressure drop across an orifice in the EGR tube. This is a good way to measure EGR flow, information the PCM would need to use EGR for reducing engine pumping losses during cruise.

EGR position sensors only monitor EGR valve position (EVP). They cannot quantify actual EGR flow. The PCM can compare the MAP or MAF sensors to the EVP sensor as the EGR valve is commanded open to verify EGR is flowing. But real-world experience indicates that this is not accurate enough to identify most EGR command faults. It can identify plugged or severely restricted passages, but it does not identify improper EGR commands caused by drifting sensors.

A variety of pressure and temperature sensors also are used for EGR feedback. None of these do anything more than confirm that the EGR flow matches the EGR command. They can not determine if the EGR flow is appropriate to deliver the expected emissions and driveability. The reality is that the PCM lacks the ability to determine if its EGR commands are correct. And these commands are not based on any EGR sensors.

The PCM uses a combination of values that come from both raw sensor values and calculated values to control EGR flow for several purposes. Most technicians assume that EGR is controlled independently to reduce NOX emissions and has no other purpose. That is incorrect. While EGR was originally introduced for NOX emission reduction in computer-controlled cars, EGR also is used to increase fuel efficiency, allow increased ignition advance and prevent heat damage to combustion chamber components. 

Fuel efficiency mode
EGR has been used to increase fuel efficiency on many cars since the mid-1980s. During steady throttle cruise conditions, EGR is used to reduce throttling losses. Throttling losses are energy that is used to create intake manifold vacuum and overcome the intake restriction of the throttle. It takes significant horsepower to create the intake manifold vacuum that occurs under cruise conditions. 

EGR commands are controlled partly according to calculated load. As load increases beyond the level required by federal emission testing, EGR commands drop off. Performance cars reach this point at a very low calculated load.

During light-load cruise conditions, the EGR valve is gradually opened much more than is necessary for NOX emission control. The open EGR valve reduces intake vacuum and replaces some intake airflow with EGR flow. The reduced intake airflow reduces engine power, but the throttle is gradually opened to replace the lost airflow. Either the cruise control or the driver does the throttle opening. 

Because the EGR valve is opened very gradually, the driver doesn't even notice that he is opening the throttle to maintain speed. The end result is that intake airflow and therefore, the fuel flow are both slightly reduced, but intake manifold vacuum and throttle losses are significantly reduced. The benefit is reduced fuel consumption under freeway conditions. This EGR based fuel efficiency mode is common on EGR equipped vehicles built during and after the mid-1980s.

Ignition advance
EGR flow can be used to allow increased ignition timing advance. That means the computer strategies used to control ignition timing are heavily influenced by EGR. 

As EGR flow increases, ignition timing is automatically advanced. Anytime EGR is reduced, ignition timing is automatically retarded. This response seems to be especially strong and quick on OBD II vehicles. It is so effective that disabling EGR will rarely result in a NOX emission failure in loaded mode emission tests. But, disabled EGR valves will usually result in increased fuel consumption and reduced power because of the impact on ignition advance.

Combustion chamber temperatures
EGR reduces NOX formation by reducing combustion temperatures. The exhaust gases that are recirculated slow the combustion process and reduce peak temperatures. Modern engines that use EGR systems are designed to perform very well with the slower combustion that EGR causes. 

When the EGR system on one of these engines is disabled, combustion chamber temperatures can rise dramatically and actually melt components. The advanced computer-controlled systems on newer cars prevent this from happening, but it still occurs on many older cars.

Idle overrides
The EGR system has a number of overrides that prevent or reduce the computer EGR commands. Some of them are well-known, but others are overlooked by most technicians. 

Engines do not tolerate EGR well at idle, so the throttle position sensor (TPS) input causes the computer to eliminate EGR commands at closed throttle. The vehicle speed sensor (VSS) and brake on-off switch (BOO) also can prevent EGR operation until the vehicle and engine are operating under conditions that tolerate EGR flow. Applied brakes, closed throttle and slow vehicle speeds can all prevent EGR commands.

WOT overrides
Most EGR commands are designed to reduce NOX emissions. So when NOx emissions are not a concern, EGR commands may be overridden. 
Cars are not designed to have the lowest NOX emissions possible. They are designed to pass federal and state emission standards. The certification process does not include testing emissions under full-throttle acceleration, so PCM strategies often eliminate EGR commands when the TPS indicates a wide-open throttle (WOT).

ECT overrides
NOX emissions are formed at extremely high temperatures. When an engine is cold, NOX emissions are not a problem. In addition, engines do not tolerate EGR when cold. 

IAT errors have dramatically different affects depending on the type of air measurement and load calculation. Speed density systems decrease EGR as sensed IAT increases. MAF systems often avoid this because MAF is measurement is not dependent on a separate IAT sensor.

EGR is not needed for emission control on cold engines, and it would tend to cause driveability problems on cold engines. Thus, EGR is reduced or eliminated when the engine coolant temperature (ECT) sensor indicates cooler engine temperatures. The ECT sensor has little or no influence on EGR commands when the engine is warmed up to normal operating temperatures. 

IAT overrides
EGR tends to increase the chance of surge symptoms. The recycled exhaust gases inhibit combustion and increase sporadic partial misfires when the engine is operating under a variety of compromising circumstances. 

When the air/fuel mixture is too lean or unstable, EGR operation can cause surge complaints. The injection nozzles on most new engines are placed in the intake manifold very close to the combustion chamber. This subjects the nozzle to very high temperatures that can cause vapor locking in the nozzle, which is prevented by the cooling effect of the intake air. 

But when the IAT is very high, the nozzles can partially vapor lock and can increase the chance of engine surge symptoms. Under these conditions, EGR commands are reduced or eliminated. Most port fuel-injected engines will start reducing EGR flow when the IAT sensor indicates temperatures of 130ºF to 150ºF. This override strategy does not apply to throttle body injection. 

BARO overrides
At high altitudes, low BARO reduces maximum engine power. In order to increase engine power, EGR commands often are reduced at higher engine loads when operating at low barometric pressures. This override usually has no effect at low to moderate loads.

EGR control strategy
Under normal engine operating conditions, EGR commands are influenced primarily by engine speed and calculated engine load. The load is calculated from MAF, engine speed and BARO. 

In engines that do not have a MAF sensor, MAF is calculated from engine speed, IAT and MAP. Load and engine speed have a direct impact on EGR commands, but MAP, MAF and IAT only have indirect impacts.

Speed density systems use air temperature, air pressure and air volume to calculate MAF. The MAP and IAT sensors provide pressure and temperature. The engine speed and the PCM's programmed knowledge of the engine displacement provide the air volume. 

Thus, MAF is calculated from the pressure, volume and temperature information provided by the MAP, rpm and IAT sensors. Any fault that affects intake manifold vacuum will skew the MAF calculation on a speed density system. EGR leaks and incorrect base ignition timing frequently skew the speed density calculation of MAF. Increased EGR flow due to leaks or sticking valves will generally increase fuel and EGR flow but decrease ignition advance. 

Calculated load is really MAF expressed as a percentage of the maximum theoretical MAF at any given engine speed and BARO. Load increases with MAF; load decreases as IAT increases. It generally increases with MAP. However MAP is affected by EGR, but load is not. Load is similar to volumetric efficiency. 

EGR commands usually are increased as engine speed increases. Load is a little more complicated. As load increases, combustion temperatures increase. EGR commands also must increase to limit those temperatures. Federal and state emission certification does not include testing under extremely heavy acceleration or high engine load conditions. So, EGR commands are usually increased as engine load increases up to a critical point. After that critical point, EGR commands are reduced as load continues to increase. 

The critical point at which EGR commands are decreased with increasing LOAD is about 50 percent on a typical car. It may be lower than 40 percent on high-performance cars and more than 60 percent on lower-powered cars. This is because a high-performance car can meet the maximum acceleration required by state and federal emission tests at much lower engine loads. Engine conditions that are not reached during certification testing can produce higher emissions without penalties, so EGR is not necessary under those conditions. 

Fault finding
All this information about how EGR is controlled may be interesting, but does it help us diagnose EGR faults? Yes, it does. 

Basic EGR commands are based on the same sensors that the PCM uses for fuel control and ignition timing. Both fuel control and calculated load are based heavily on MAF. When MAF is undercalculated, both fuel and EGR delivery will be reduced at light to moderate loads. When a MAP, MAF or IAT sensor causes MAF and load to shift fuel metering, EGR and ignition advance will all shift. The shift in fuel delivery will be sensed by the oxygen sensor and corrected by the PCM, and the fuel trim records will reflect the fuel correction.

Under light to moderate loads, positive fuel trim numbers (or high block learn numbers) indicate that EGR has been reduced and ignition advance has been increased. Negative fuel trim numbers (or low block learn numbers) indicate that EGR has been increased and ignition advance has been reduced. 

Fuel trim also is affected by fuel pressure and injector restrictions. Whenever fuel trim records are higher than about 10, it is a good idea to check fuel pressure and verify the accuracy of IAT, MAP and MAF.
Comparing scan tool values to a vacuum gauge can validate the MAP sensor, but IAT and MAF are a little more difficult to validate. The easiest way to validate the IAT sensor is to check the scan tool value before starting the engine first thing in the morning. Under this condition, IAT should equal ambient temperature. 

The BARO value also provides clues about EGR commands. The MAP sensor is usually used to record a BARO value during engine start-up. Before the engine cranks, manifold pressure and barometric pressure are equal. If the MAP sensor has drifted, the BARO value that is stored at start-up also will be off. Cars that do not have a MAP sensor will calculate BARO from MAF, IAT and engine speed during low speed, WOT operation. This is actually a reverse of the speed density calculation. The calculation actually provides a MAP value, but under low engine speed WOT conditions, BARO equals MAP. 

If a cars' BARO value is wrong, the MAP, MAF and IAT sensors should be checked for accuracy. Technicians should understand that restricted air filters, restricted exhaust and certain valve timing and camshaft problems also can cause the stored BARO value to be incorrect. When evaluating the datastream BARO value, compare it to other cars in your shop or the BARO value that is available from a state-certified emissions test analyzer. The BARO used by television and newspaper weather reports is a corrected value that should not be used for automotive diagnosis.

When troubleshooting EGR systems, most people are more comfortable checking the mechanical bits first, and fortunately that's where most problems lie. But when the passages are clear and the valve opens and closes properly, then the task is to determine if the valve is operating as commanded and if the commands are based on good sensor data. Understanding the operating strategy will help.