I had this exact same problem. It was bizarre and the only workaround I found was:

1) Start a new game and make a manual save right before getting on the lifeboat (skip all of the rescue options)
2) Let the cutscene load into Fort Joy (this worked for me when I didn't try to save anyone else)
3) Once you're already in Fort Joy, THEN load your actual save and it should work.

The good news is, it got me through Fort Joy with minor annoyance and the next area seemed to work fine for Act 2. The bad news is, the area for Act 3 is now doing the same thing, so...