Any custom UI things installed, skinning-like add-ons?
Try toggling "Reduce Transparency" on and off to see if that shakes things.
If that doesn't work, try Terminal:
defaults write com.apple.universalaccess reduceTransparency -int 0
ADD: re: defaults above, first do following to see what OS X thinks it's set to:
defaults read com.apple.universalaccess | grep reduceTransparency