When you beat him into submission, did he then give a little speech about not being in control of himself and seeing through someone else's eyes? If not, that may be the problem: the quest stages may not be updating properly.
This sounds like a good diagnosis.
There's also the possibility that when you get back to the fort, Vampires are attacking, which might set NPCs into fight mode. Probably not, but it's happened to me (outside the fort).
EDIT: Re-reading your post, my suggestion doesn't sound right, actually.
Still, it's a shame that the OP is jumping on Bethesda for a glitch when the first half is pretty much how the quest is meant to play out.