The rooted Nautilus window does not crash. But it seems that any
application does intensive io, and is not root, does in fact crash.
Although just a hunch, I have a feeling that this might be kernel
related. I reported this bug, after the second time that it had
happened, on my Windows XP installation, so first I need to reinstall
Ubuntu, and then setup libvirt, which is really easily thanks to the
ubuntu-virt metpackage, and then I can be more detailed in my reports.

Also it seems to change all the permissions on the file system, so it
really hard to copy files back and over.

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file system drops dead when copying files between a rooted nautilus window and 
desktop
https://bugs.launchpad.net/bugs/245081
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