David,
I chased a similar problem on my 3-rotor back when it was barely out of initial flight testing. Tried a lot of things, but nothing seemed to fix the random re-set of the EC-2 MAP table. Someplace I heard about voltage spikes originating from the starter solenoid. I installed a large diode across the "+" terminal of the starter solenoid and haven't had a problem since. The culprit may be different with your a/c, but I would be very suspicious of anything that could generate voltage spikes. Also, check all of your grounds thoroughly.
Good Luck,
Mark S.
P.S. The first thing Tracy always asks is, "Did you try the B-controller?" How does the B-controller MAP look?