Hmm, sounds familiar (and, at no particular time of day or night).
I've had this happen for segments of the board (& on rare occasion the whole board) when, my cursor's button is depressed as I slide the cursor over a couple of squares and/or when I touch my right mouse button. [PC, XP with I.E.]
So far, I've been able to undo this effect by left clicking two or three individual squares.
For some reason this seems to happen more at night. I go to play moves in a tournament and there is a small blue and white board over the regular board. It does not allow me to play my move. I have a mac and use safari.