What type of code scanner are you using? Is it one of those Actron units with the 2 switches on it? Also,did you plug in both the multi-terminal & single terminal connectors to the scan tool?
Plug the scanner in (both plugs).Make sure the switch is in the off (Standby) mode before you plug it in.Then,first turn the key on but don't start it.Now turn the scan tool in test mode and see if it gives you any codes.Turn the scan tool off,start your car and let it run for a few minutes.Now turn the scanner back on and your pcm should run a test.You'll know this because the engine will speed up for about 1 minute,then it'll slow and should flash a code/s.
Maybe the LED is burned out in your scanner?? Also,if the engine speeds up during the Key On Engine Running (KOER) test,then I highly doubt your scan tool is faulty...except the dumb LED.Try the Test Light method if none of that works for you.