I just ran into a really weird problem on a computer I was troubleshooting at work. Items on the desktop were appearing on top of each other, and were not selectable. Also when the user tried to open things from an application, several mounted volumes (CD and network) were not showing up in the open dialog box.
I went in with the finder, and finally discovered that there were two copies of Finder.app running at the same time: one from the startup volume, and the other from a HD that was remote mounted (AFP).
My solution was to simply kill them from a ssh session from my computer, and let then let a copy re-launch. We then had to quit out of a couple of applications, and things were back to normal.
I just thought that I would put this out there in case someone else runs into it.