Certain and random NPCs are running away from me, screaming, while my weapon is holstered and my pants are zipped. I can understand Gary running away at first sight, given the circumstances that ended our last meeting, but other doctors in the hospital are also just running away for no reason.

Pretty much just the way the game was set up I guess, with it not being free roaming the level designer at the time probably didn't think to make sure the AI was set up to treat your normally if you are not packing heat. Sort of thing that's easily fixed with a mod but would it be worth it?

Mine does not do that. Maybe a re-download?

My copy doesn't do that either. It sounds like the game thinks you have your pants unzipped.