I'm not used to having a roommate; it's been five years since I've lived with anyone other than myself. But more importantly, my roommate does not appear to be used to having a roommate either - my very presence scares him. If he doesn't notice me come home and than sees me walking around the apartment: he yells in fear. If he comes home and I shout "hi" from my bedroom: he yells in fear. If he comes home and I don't shout "hi" from my bedroom and then he sees me: he yells in fear. If he comes home and I am sitting on the couch in the living room: he yells in fear. If I walk in the front door and he's sitting on the couch in the living room: he yells in fear.
There is pretty much no way for him to see me in the apartment and not yell in fear. I'm afraid I'm going to give him a heart attack. We discussed how to prevent these shocking confrontations and he suggested I call him every time I am about to come home, though, of course, this wouldn't account for the times when he leaves and comes back and I am still there. I'm not about to register my comings and goings with my roommate, so he may just have to get used to being scared by my existence and I will have to get used to a lot of yelling.

And what of the tried and true college philosophy of having a little white board on the front door with a smiley face on it when you're home and a BIG smiley face on it when girlfriend is home with you?
As your former roomate, I am trying to recall if there was a reason to react this way to you. I can't remember, but it may have had something to do with wardrobe. Have you been wearing pants in Manhattan?