Thanks guys, it doesn't catch your fingernail at all. It's more that if I run my fingertip over the area, I can tell where it is as it just feels different. Maybe marginally less smooth (the trunk lid has paint sealant on it, including this area).
This is the best picture I managed so far, I'll try and find my old camera which is better at close ups.
http://img193.imageshack.us/img193/8752/paintch.jpg
The area in question is between the reflection of the garage door opener and the window, closest to the window. From this angle it looks like a smudge or fingerprint on the paint, but from other angles it's completely invisible. When you get closer it appears to be made up of many smaller scratches. I'll try and get another picture showing the detail of that.
I already tried a very light application of meguiar's paint cleaner, and meguiar's scratch-x, neither of which did anything. But, I didn't really polish it hard in case I made it worse.