Ok, for the people who encountered similar problems- these happen when saving the game at a very specific point (after picking your background but before finishing the prologue). I put a definitive solution to this shit with the 0.6.1.2 version. If your save file is affected, just downloading the new version will solve it.
I'm super sorry you encountered this, it's such a specific border case that none of the dozen or so people doing playtesting the build caught it