I've been having this problem recently as well. One of our clients is seeing it several times a day. The problem results in the cursor stretching to twice its normal height and the Y cursor space seeming to double. This means that you have to click at the bottom of the screen to hit something that is displayed in the middle.
I've found that this can be fixed by going to a virtual terminal (Ctr-Alt-F1) and then back to X (Ctr-Alt-F7). This is a major problem for our client, however, as they can't be expected to do this very often.
Has anybody seen this before? Any ideas?
I can post my config files if necessary.