I know it's not the pickup height, I've actually checked it like a half dozen times because a while back there was a problem with the bridge pickup being too high.

I'm not too comfortable messing with string action, although I had to mess with it a while back because a common problem with the guitar model I have is loose pickup bushings. It's fixed now courtesy of 2.5 ton epoxy, but the entire bridge was pretty much unattached to the guitar for a while, besides being held in place by string tension. When I got the guitar the strings were about half the distance from the frets they are now, hopefully that can be set right when I take it in.

I'm not in the same town I bought the guitar in, hopefully that doesn't change things too much.