After running s-c-desktop, I see on stdout: Window manager warning: Working around an application which called XSetInputFocus (None) or with RevertToNone instead of RevertToPointerRoot, this is a minor bug in some application. This is 1.0.14-1
Hmm...I don't see this on my test machines. What version of metacity are you running? Havoc, what does this message mean? As far as I know, system-config-display isn't doing anything besides just forking metacity to provide some window management functions.
that was stock FC2, so it should be metacity-2.8.1-2
Message means what it says - some app called XSetInputFocus(None) or with RevertToNone. gdk_window_focus (NULL) may do this, I'm not sure. Metacity doesn't know which app did it though, so can't print out the blame. It's possible this could be a metacity bug/confusion, but probably not likely. Anyway, the bug is minor in most cases. Basically if the focus ends up set to None then you can't use your keyboard anymore (this is major), but it ends up minor since metacity moves the focus back somewhere.
Since I'm unable to reproduce this on my test machines, I'm going to assume that some other application triggered this message from metacity. Closing as 'worksforme'