So even on a pure factory tune/snail, never altered at all, when one so much as changes out the battery, this must be re-calibrated??
Do the tuners, whether it is a flash tune, or a 'full works' tune, as a matter of course, put any type of re-calibration of the misfire counter?
IF not, there are A LOT of people out there running around without operational misfire counters, and potentially running into the very same problems you have cataloged here.