From what I can read it’s a common issue for many people using Ubuntu 10.10, at least among the users of the 64-bits version. There are two bugs reported in launchpad: here and here.

After several months without problem, I just experienced this issue… and the two solutions given in Launchpad (aptitude reinstall gnome-settings-daemon and sleep 2) don’t help at all.

So, how to deal with that? Well, it’s simple: just open a terminal window and in it write:
$ gnome-settings-daemon

Now the theme is restored, but the icons in the file manager still look bad. That’s because of Nautilus the file manager. You have to kill it. Yes, kill it:
$ killall nautilus

So Nautilus will be restarted after that, with the right icons. You can now close your terminal window and go back to a normal life.

I hope the Ubuntu people will fix this issue before the release of the next version, Natty Narwhal, which should be released this month.