I would be afraid there is some underlying problem at work here. Changing ECUs or using an AP isnt going to change that if thats the case. Can you do some continuity testing on the ECU and obdii port? Maybe there is a bad connection somewhere causing the issue.
I still dont understand why it would report a successful flash. Next time you need to save the log from the flash so we can take a look at it. It should be flashing, then confirming that the new image on the ecu is the same. I would think if anything was ending up corrupted on the ECU after the flash, that this verification process would catch it and spit out an error.
IF (and a big IF) this is exactly whats happening (which we cant verify without a log, or a copy and paste of the output), it's scary to think that ecu flash can report A-OK and have the ecu end up bricked.
Does ECU flash pop up a warning if you try to flash an incompatible image to the ecu or does it just flash away? I dont think I want to test it :P