Mine does that occassionally too. Did you happen to leave it sitting for a while after it flashed?
80% of the time when mine does it the car is fine, I had done and Vcm read after closimg the write box down while is saying "retrying"
and after comparing the tune i was trying to write and what was in the PCM they are 100% the same.
I have had the car run like a hairy goat too like you described.
OT but are you able to log TPS% and Boost on Ba's?