When my machine is working fine and dandy, I usually copy the Window Layouts folder in Users>Library>Preferences and paste it in my documents. This way if I need to get rid of my prefs because the MacPro is running badly I still have an uncorrupted layout folder to drag and drop into the Window Layouts. I have 6 personal settings that I use and this has worked great the last time I have had to delete prefs.
I did have a problem when we upgraded to Leopard and it looked like FCP did not like my prefs from the last version. So I did have to make new Window Layout settings which is the one I have saved now in my documents folder.
good luck,
Victor