In my experience
it sounds like you need to run the acceleration manager found in
MENU-> SETTINGS-> acceleration manager, select aiglx and then wait for about 30 seconds (cause the acceleration manager takes some time to get all of the settings working) then re-start your Xserver
I'd run it as root, also if you have "absolute" monitor positioning enabled in the nvidia Xserver settings for your second monitor, I've found that (at least for me) the desktop acceleration won't work but this is providing you have a second monitor.
finally, if you have an ATI graphics card the desktop acceleration might not work right
I hope this solved your problem, feel free to ask if this doesn't help
quick edit here
also in my experince, the desktop will turn black for like 5 seconds and then go back and thats how you know if desktop acceleration is working, or at least thats what my desktop does with me, and the command for starting compiz is "compiz-start" minus the quotes. also, don't forget to re-start the Xserver