I'm looking for help trouble shooting an issue.

I just had an engine out on a buddies 997 TT. After putting everything back together, I have an issue I've never experienced before. I went to start the car and everything powers up, but the engine won't crank over. I connected the Cobb accessport and it says "cannot connect to ECU". Now, if I remove the negative terminal on the battery for 10 seconds and re-connect it, the ECU is seen and the car will crank and start normal (but only 1 time). As soon as you turn the key to the off position, it loses connection to the ECU and the engine won't crank until you remove the battery again.
I've by-passed the clutch switch to rule that out. It seems like a ground issue, but the engine ground and battery ground are clean and solid. I was planning on removing/re-installing the starter wires to make sure they have a solid connection.

Is there a "breaker" fuse or relay that could be getting reset with removing the battery? Has anyone experienced this before?

 

It does sound like the issue is on the ECU itself.. What is the current stage on the ECU?