TunerPro Glitch

Hey everyone,
Has any one had a glitch with either Tunerpro or the Autoprom before?
Since I started using these systems on my previous engine and the new engine I have been experiencing a symptom that would indicate power loss or a ground fault to the ECM. Ive been going crazy trying to find a fault in the vehicles harness until last night, I was waiting for my pizza and thought about when the problem began. It was when I first used the autoprom with tunerpro so for shits and giggles I swapped the memcal module with a stock one I carry as a fail safe.
On the the trip home not a single problem except for the tune not being correct for this engine.
When using the auto prom the symtoms are like the ignition is cut for a split second, the following things happen- TCC drops out, map jumps to 100Kpa, ingnition and injectors cut out and one other strange thing is when holding the throttle steady the TPS percentage drops to zero but the voltage stays the same.
If any one has a reason or a fix for this could you let me know please.
The ECM is a 16197427
XDF $OD vTP5 251
ADX-A217 $ODTP5 250