http://wiki.compiz-fusion.org/Hardware/NVIDIA
Given when this is happening, I wonder if it might be a problem with Nautilus, though why it should disappear when you switch off desktop effects I don't know.
Have a go at this. Open a terminal and (with effects switched on) type:
Code: Select all
nautilus /home/yourusername/Documents
See if you get any warnings and if possible copy them (or note down the basics if you get another freeze) and post the results here. That might give us a clue.