yeah, our typical process is if she shifts or runs bad, load the bone stock file. If it fixes it, then the next step is load old tune back in with stock uS, and torque tables. If it runs good then, the next step is to start adding the tables in 1 by 1... If it is something out of the blue that doesnt make sense, we just put it in our little notes bin and refer back to it as needed. It would be interesting to find the specific cause. Sometimes the ALLI hunts for a "out of range" tq value..we try to keep everything at or under 812 (lbz/lmm) and everything else 590 or under if needed. 100mm3 tops on them and 120mm3 tops on lbz/lmm.
hope this helps some others that may have these types of issues reading this thread.
Cheers,
Kory