I found a solution for my situation. I have Ubuntu Natty. When I loaded a U3 type flash drive the desktop would freeze up, etc.
From synaptic I downloaded "u3-tool".
Couldn't find much documentation for it, until I found this code that worked for me:
sudo u3-tool -p 0 /dev/sdb1
sudo u3-tool -p 0 /dev/[your device name]
That removed the "u3 crap" but maintained the files in it. It's easy to remove the remainder manually
Edit: May 23,2011 I Must be a thread killer