I believe xinput looks normal, but I can post some logs if anyone needs more information. I'm using compiz-fusion, Xubuntu 12.10 x64, nvidia-common, and xorg-edgers. Where should I go to look for more information when this problem occurs.
This issue occurs even if I use xfwm without compiz.
My current workaround (which isn't a great time) is to zap the GUI and re-log in (with CTRL+ALT+BACKSPACE).