Well, it is only an idea so far...
Please try to find out, from which date/time your last career files are.
Not "game time", but real time in Windows Explorer.
They should be in C:\My Documents\... or where ever you have kept your personal files.
Maybe there is
now after the rollback a problem with one of the .cfg files there. Some information like last mission etc. is kept there; there are some .tmp files as well.
Maybe they collide with the game now ?
Edit: I remember I had this phenomenon years ago in SH 3 Stock. Even the deck crew was turning around with their arms spread. I made a fresh install as a solution. I do not know the reasons for that behaviour. It was an unmodded SH3...
Edit: Wasn't it "Default Poser Status" after time compression on the bridge?
I think it was gone after a dive...