Used the o-fficial 3.6 installer with all the various bells and whistles. Decided to play through the main campaign and bug-hunt.
No problems during the first training mission. At the end of the second, when jumping out, my ship didn't vanish into the warp portal--the model simply passed right through it, until the warp closed and I went to debriefing.
I know someone else reported this problem fairly recently, but after bonking around the search for about fifteen minutes, I couldn't find the right thread.
What puzzles me is that this didn't happen during the first mission, and might have been nothing more than a random futzing of code. I'll keep playing and see if it should pop up again.