Issues after flashing to my PCM - momentarily

[Sparkey]

After I flash a new file to my PCM, my car will run like garbage. My BARO sensor is reporting 98kpa, after I run it down the road and push it into boost a couple times, the BARO works it's way down to reporting ~62kpa and wont hold an idle. After letting the car sit for ~30-45min, I can hop in the car and it will run great. At fist I was thinking bad MAP, but usually those are either good or bad I thought. Now I am wondering if my PCM is about to take a shit.

This has been going on for a while and I have just been dealing with it, but now I'm just plain sick of it. This is very repeatable, it happens every time I flash, no matter of what I am changing. Has anyone seen this or have any suggestions? I do not want to start throwing money haphazardly at this situation.

Technicals: 2005 Cavalier, supercharged, 2.5Bar Bosch TMAP
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[planethax]

Try disconnecting Battery after writing the file and see if the issue is gone.

[Sparkey]

Flashed the PCM again today, this time disconnecting the battery for 15 min after the write was complete. No change, the problem persisted.

[Sparkey]

nobody else has any other suggestions?

[mecanicman]

The problem is the tune file. Its so far out of wack that it wont run right until the fuel trims have had time correct. Start over.