Comment 34 for bug 151674

I had a similar problem. The issue was that my two monitors were at slightly different refresh rates, despite the fact that I set both to 60hz. If you can set your monitors to the same refresh rate exactly, then you should be fine (check each monitor via its own interface). Otherwise, if you are like me your monitors don't sync at exactly the same rate (one was 60hz, the other was 59.9). In this case, running one compiz instance to manage both monitors results in vertical tearing with or without sync-to-vblank enabled. When enabled, single tear moves down the screen; when disabled multiple tears appear and disappear hap-hazardly... test by dragging a window left and right.

Solution is to run two different compiz processes, one for each monitor. Add the following script to your gnome startup:

#!/bin/bash
DISPLAY=:0.0 compiz --only-current-screen &
DISPLAY=:0.1 compiz --only-current-screen &

Hope that helps