Comment 2 for bug 421392

This actually is a hardware limitation. When your Virtual size is larger than 2048 in any direction DRI is disabled so of course compiz and any other 3D apps are either not going to work or run slowly. Based on your issues with scrolling it sounds like it also disables all other acceleration as well.

Basically, you cannot have desktop effects (or desktop acceleration of any kind, apparently) and use a second monitor or even an xorg.conf that would allow you to plug in the second monitor at any point.