Anyone have any clues because I just don't think addon....is the cause?
It looks like your FSX.CFG was corrupted. Yes, the Addon Manager reads it to allow the various tweaks, and if you press the "Save to FSX" will write it too, but nobody ever reported a problem with it in the many years it has been out.
MAYBE, another add-on that access the FSX.CFG was either trying to write it at the same time that you ran the Addon Manager OR it caused some kind of corruption or introduced a syntax error, and that might have forced FSX to rebuild a new one from scratch, with all default settings.