In gdm, the login window resizes itself shorter and taller as its contents change. Whenever it resizes shorter, the newly-exposed area behind the login window is solid black, instead of showing the actual background image.
(I'm assuming this is xorg's fault, not gdm's, since gdm looks like it's doing the same thing it was doing in F11, and it works fine there.)
Ray Strode said this is actually a gtk2 bug.
I've fixed this in the latest build