I have a similar situation, using a Toshiba Tecra laptop with Nvidia graphics and Ubuntu 11.10. Especially when I use a second screen, which I do most of the time, my computer takes a long time after logging in to become responsive. It reminds me very much of a Windows system! Starting up any application right after logging in takes ages (. On top of that, I also experience the intermittent unresponsiveness of keyboard and mouse. The "remedy" is to simply wait a while (like half a minute) for it to become responsive again. I do suspect the Nvidia driver because it has given me a lot of headaches to recognize my second screen correctly.