Usually when guys disappear completely like that you can find them on the other side of a door or in the next area. If this is an area you can't get to it's a problem. Try changing tactics so he doesn't run away. It would be difficult though not impossible to figure out if any mods are causing this. It probably isn't any mods, just the tactics you are using though.
Okay, thanks for the reply smeagol. Strangely enough, there is no other room. It's just a black doorway that doesn't actually lead anywhere (it's the final battle in hell). I'll keep messing around.
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