Thanks girls, I have narrowed it down to in his bedroom and the immediate hallway out the front of his room. That's where he seems the most scared. He still says he's scared in the living room but I suspect it's because he's usually just come from the bedroom. I feel no malice in any areas of the house, sometimes I feel like I am being watched but that's just my paranoia LOL
I wholeheartedly believe that children can see things that we can't. If he's scared of a room, then there's a reason for it: whether it's something tangible (such as a toy he doesn't like or a shadow) or something intangible.

I remember being terrified of my Nan's hallway and end room. It wasn't until I was grown up that my mum (and her sisters) fessed up that they also grew up being scared in that house and my Nan has even since said that she didn't like it. Was it because it was dark or was it something else.

Just trust him. Why should our children be scared of something just because mummy or daddy can't see it or understand it. Just because it's not real to us it doesn't mean it's not real to them.