Here's an article from Gamasutra discussing the Uncanny Valley as relating to character interactions.
"...a Tickle Me Elmo doll pushes a lot of our "cute" buttons. However, when it's set on fire and continues to giggle, kick it's feet and shout "Stop! Stop! It tickles!" while it burns into a puddle of fuming goo, it seems horrific, profane and hilarious by turns."
Aside from the fact that I have always loathed Elmo, the quote above really pins down why I have a very hard time relating to automated characters (NPCs) - they almost always end up in situations where they behave as "things" instead of as people.
Found a journal of someone doing their PhD on this. Lots of pictures and ideas. I'm not sure how much the theory relating to something being corpselike or resembling someone with a facial birth defect works for me. I don't find bodies disturbing unless they belong to someone I knew. When I've been around people with facial deformities I haven't felt disturbed, I'm more concerned with learning how to reliably read their expressions.
What does creep me out are things like Duracell's Puttermans, or the current Burger King. I don't think it has to do with masks, clowns don't bother me. And I'm too old to have been scared by someone with a Botox treatment when I was a child. ;)