You could try Feliway. It comes in a spray, diffuser and collar, which may make her feel a little less nervous. It is phermones, which calm the cat down.
I had this problem with Moosey when we first got her, and although she has pretty much gotten over it, she still has those times when she freaks out and runs under the bed. She still doesn't like to be around my roommate.
What I did: Any time I was the only one home, I would shut the door to our room so she couldn't run in there under the bed. I would do this when I was just sitting there watching TV or doing laundry, anything that caused limited mobility so she could walk around and sniff and rub her scent on stuff. After a few weeks, she would start to come out on her own when it was just my boyfriend and I, but always run when my roommate came around. (he isn't home very much) Now she will sit in the living room when he is around, but wont let him pet her and if he makes a noise or moves, she is off running.
Lately she has been okay with other people coming around as well, but will still run if they move and will not let them pet her. (The only person she likes besides my boyfriend and I is my roommates girlfriend, which makes me think that she likes females more than males)
Moosey warmed up to me pretty quickly, but she is also my cat. When she was in her safe spot under the bed I would talk to her in soothing tones and say "good girl" "pretty girl" ect.
As far as medicine goes, I would say you are just going to have to hold her down. The first time I clipped Moosey's nails, she was so sweet, which made me really excited, but the next time she was not having it, so I had to have my boyfriend help hold her down. She was pretty upset for an hour, but got over it quickly. It is sad that they don't realize we are doing this for their health, Poor babies.
Moosey has also always been very affectionate in bed. This may have something to do with you laying down, which makes her taller than you or the darkness. (this is just a guess)
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Last edited by grrawritsjordi; 02-11-2013 at 03:33 PM.