I've been experiencing the same since formatting and installing Lucid 64bit. I have two 24" monitors each having a resolution of 1920x1200. I see the performance issues using both compiz and metacity compositing, so that made me thing it was an nvidia driver issue. I've installed the 256 nvidia drivers from the X ppa but am still seeing issues.
One thing I noticed is lets say i have a clean desktop. I open a terminal on each monitor. Now lets say I fullscreen the left terminal and 'less' a large text file. I can mousewheel scroll up and down very smooth. Now if I fullscreen the right terminal, then go back and try scrolling the left terminal again, it's horribly choppy.
I can start pasting logs if anyone needs. This is my work machine that I rarely reboot, but I could if I needed to get clean logs.
UPDATE: After playing around for a bit, I realize it doesn't much matter where I have the second fullscreen window (ie. it can be on a different desktop). But as soon as I fullscreen another window, my first one I test scrolling in starts bogging down.
UPDATE2: After more playing and a couple reboots trying more driver changes (back to running 256 though for what I'm about to say)... I boot up and start setting up my work environment across my 6 virtual desktops (2 screens each). I get 7 terminals open (one fullscreen per desktop), eclipse open (using a full 2-screen desktop), 3 instances of chrome (one full desktop) xchat and empathy. After opening each app/window, I check performance with the scroll test mentioned above. I get all these windows open and everything is still fast. I then get distracted catching up on missed IRC chatter for a couple minutes, then i go to do the scroll test again and it's horribly slow again! My uptime at that point was 9 minutes.
SYSTEM: Dell XPS M1530
GPU: GeForce 8600M GT



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