I'm also having an issue with Fane's questline at the moment, though it takes place in the later acts rather than Act II... I was able to get through Black Pits without any issues here.
I have made a thread (albeit in the wrong forum section) about it - though be warned there are slight spoilers
http://larian.com/forums/ubbthreads.php?ubb=showflat&Number=622313#Post622313
Hopefully it'll be looked into.
