If an app (for example gmc) changes the behaviour of the mousepointer (modal mode) and does not restore it to normal there's no way to get the mouse to return to normal mode and to click or focus on anything.
I'm not sure what the right component for this is but I do not believe it is XFree86. I cannot reproduce it at all. Could be a window manager bug as well I think. Actually that sounds more plausible. What window manager are you using?
I wasn't sure about the component either, but I figured I had to pick something. I was using Sawfish at the time (0.37 I believe). I have switched back to enlightenment right now but as I recall I haven't had this bug in this WM yet atleast.
Ok, well it seems resolved for you now then. For the record, we have never released that version of sawfish. Our current is 0.36 so if you use a newer version, you're best reporting the bug to the sawfish team. Take care! TTYL