Well, I had exactly your problem in one of the very early patch versions - I couldn't kill that steel scorpion <img src="/ubbthreads/images/graemlins/shame.gif" alt="" /> - fled and then had hanging cutscenes.
Have you got a save prior to entering the underground cemetary section? I'm just asking, because I haven't read about "hanging" prob for a long time on this forum. I didn't know this still exists if you patch up later <img src="/ubbthreads/images/graemlins/confused.gif" alt="" />
Kiya