Sometimes I get something similar with my hard drives. The Finder side bar shows the drive's custom icon, but it appears on the desktop as the bare drive icon. Simply clicking and dragging the icon around even by one or two pixels causes the icon to reload.
I don't remember if I've had that specific issue with regular files, but it might be worth a try. It'd be easier than reloading the Finder entirely. I'm not sure why it happens, either; I've repaired permissions many times before, so that's not the issue (for me, at least).