It has something to do with the desktop picture. I know, that sounds crazy, but hear me out.
One of the ".db" files in the dock folder was "desktoppicture.db." When I deleted it and rebooted the Dock, it reverted my desktop picture to the Hallowen image I had months ago. I've changed it at least twice since.
I suspect it has something to do with the way Launchpad overlays the desktop picture, without the icons/dock.menubar, etc. It must reference the image itself, instead of simply overlaying the Finder.
Could changing the desktop (especially often) maybe freak out whatever references are kept to the correct background image in Launchpad, thereby throwing off the whole screen draw?
To reset the Launchpad icons (and possiby your desktop!) 1) Go to ~/LIbrary/Application Support/Dock, and delete the files there. Then open Terminal, and enter "killall Dock" (capped just like that, no quotes).