I'm not sure what is going on with the ECM, it seems strange that a brand new one would be messed up like this, but the shop doing the work is extremely experienced in modifying LS1 engines, so they know these things inside out, and went through the complete troubleshooting flow chart and came to the conclusion that it had to be a second bad ECM. They checked every single connection and all the fuses, etc.
The odd thing was that the new ECM worked for half a day. I just hope the new ECM that they install tomorrow morning does the trick!
On the plus side, I will most likely get my dyno tuning redone yet again for free! It'll be the third time they've redone my dyno tuning for me at no charge.