I see very similar issue, but with Core i7 Sandy Bridge, Intel HD Graphics 3000 built in, which makes me think - this is nothing to do with NVidia, but rather with Compiz. The desktop effects like moving between virtual desktops is buttery smooth and the suddenly it goes very jerky and slow. It stays this way, until I go into CCSM and disable unity plugin, then re-enable it back - it is buttery smooth again.
I see very similar issue, but with Core i7 Sandy Bridge, Intel HD Graphics 3000 built in, which makes me think - this is nothing to do with NVidia, but rather with Compiz. The desktop effects like moving between virtual desktops is buttery smooth and the suddenly it goes very jerky and slow. It stays this way, until I go into CCSM and disable unity plugin, then re-enable it back - it is buttery smooth again.
I think, this is related - https:/ /bugs.launchpad .net/ubuntu/ +source/ unity/+ bug/888039
Some details about my setup: I'm using 2 displays of different sizes and resolutions: 1920x1200 + 1600x900.