wsphon,
I think he did have the EBCM reprogrammed under warranty. after that, he had his ECM programmed by an aftermarket tuner. The only place that can / should tune the EBCM is the dealer. I had the same reflash of the EBCM done a month ago and it solved the issue I had, for now at least.
Sol-Stuce,
The first thing I would do is contact the aftermarket tuner. If you were having no issued the day you took out your ECM and now you are, there is something wrong. Also, they can return you ECM to stock and see if it goes away. I understand why you withheld the name of the company, but that being said, if they are a comany worth their salt, they will work on this problem until it is fixed or return you to stock and refund your money. You paid for a service, it is causing you problems. Go back to them for help. That would be my step 1. A simple phone call may solve all your issues and have you going fast.
GJ