i know it's a little late for a reply, sorry
had to get a new HDD.
i just got FC3 freshly installed again.
the setup's exactly the same as the previous hdd.
you're probably right about the graphical filemanagers, the contents show up on when browsing through the shell.
weird things just happened. i managed to open the folders by double clicking on them, then pressing the up arrow of the filemanager, and the contents showed.
but after a few times of doing this, the entire thing crashed, a window popped up saying nautilus crashed. i can reopen the filemanager, and all the icons on my desktop disappeared too.
can log out either.