Don,
On the QMX that has distorted audio, please turn off the 'phase predistortion' option in the SSB menu, and see if that corrects the distorted audio.? If it does, please look at the calibration phase error plots for each band, and see if any of them are incomplete, i.e. they don't go all the way on the x axis to ~2000 (9V build) or 2600 (12V build), and see if that is the band where you heard distorted audio.? This data may be helpful in understanding what is happening.
?
v006 does have further changes to the calibration, so you may want to try to load _006 and re-do calibration, at least on any bands with incomplete plots.? But in general, I don't think you have to do a factory reset or update calibration when loading any of these new versions.
Stan KC7XE