This is one problem that can drive you nuts. I've seen it a lot of times, but for some reason, it seems that one simple fix does NOT always work.
I agree with whoever posted that Tweak UI is a great, great tool, and that SHOULD clear it up. But if not, then it gets a bit weirder. In some cases, Tweak UI actually screws up the icon cache! If Tweak UI doesn't work, here a few ideas...