Acert c-15 need help!

Here is the story. Had a platinum rebuild done and had to get my ECM reflashed. I had another CAT file in it, but it would void the warranty of the rebuild. After a few days of running it the truck began to run rough. I went in to the shop and the ECM showed that injector 3 and 4 had reverted back to the previous trim codes. After changing them back to what they were supposed to be the ECM would lose the codes and revert back to the old ones if the key was cycled off. Replaced the ECM and it did it again as soon as it came out of the 24 hour test mode only this time showing injector 3 and 4 not programmed because it was a new ECM. Replaced the ECM yet again and it did the same thing. Tried to clear it out and it wouldn't. Had to install a different file in it from another truck and then clear it out. Then manually put in all the information and it seems as though the problem is back. Going to the shop in the morning to find out for sure. They don't seem to have an answer. Anyone have any suggestions? Thank you!