Using TLink to check "stuff" while running the stock chip is a good idea. Check that all the sensors are outputting normal values.
By the way, which Thrasher chip are you using? The reason I ask is, I was recently asked by a friend to modify his Thrasher (9230) and while doing so, I found three bugs in the code. I'm not sure if the same code is used in all versions, but it might be. One bug affects knock during trans shifts, one affects the Integrator's ability to properly track the O2 sensor (during closed loop), and the third affects AE for a short time after the car is started. None of them are major show stoppers though.
If I have the Thrasher version you're using, I'll look at the "start engine" code to see if anything is unusual and I'll check for the 3 problems just mentioned. I'll let you know.