LOL, that's a weird issue. I had a different, but possibly related issue that I still haven't figured out. It appears that some of the images that the Dock uses to display the backgrounds for the names of files/applications and for the Stacks backgrounds get lost or something on occasion, and so I get missing corners or backgrounds or sometimes the names themselves go missing. I think it was something I did in customizing the Dock, except that I then copied back an original unmodified Dock.app and it continued doing the same thing.
Good luck finding out the problem, let me know if you find a solution!
jW