I've noticed that it only affects your boffs that are on station at the moment the bug kicks in. Whenever you get a new boff, that boff isn't affected by the bug and can be placed.

Now that I think it over, when you're forced to switch ships for the purposes of a mission, the game hasn't caught up with the fact that you're back in your own ship. AFAIK you can't use boffs on a ship you're forced to fly in a mission, and when the mission completes, the code still has you in the mission ship. Changing ships seems to reset this "marker" (being that I can't think of a better term) and sets you to the correct ship, allowing you to assign your boffs freely.

Just my hypothesis based on the available data.