Think this bug is just part of Oolite (even if you have no OXPs installed). It seems to strike most often when a mission variable changes. I've hit it when playing Thargoid Plans and Deposed. The best safe guard it not to overwrite your Commander, but save as Jameson1, Jameson2, Jameson3 (and repeat). Once the bug strikes, the commander is screwed. But if you hit the bug on Jameson3, load up Jameson2 and you've only lost a bit of progress.
OXPS : The Assassins Guild, Asteroid Storm, The Bank of the Black Monks, Random Hits, The Galactic Almanac, Renegade Pirates can be downloaded from the Elite Wiki here.