This started happening after the OSX Mavericks update.
With the visor hidden, I try sliding one space (to the left or right, doesn’t matter). During the slide animation, a black box the exact shape of the terminal window appears where it normally appears on the new space as it slides in, but disappears when the animation stops.
If I close TotalTerminal, this doesn’t happen, so I’m assuming it’s the terminal Window not meeting some expectation relating to hidden windows that keeps them hidden during space transitions.
This happens with 1.4.4.