sounds like you are having trouble with Expose/Spaces getting in the way of FCP’s function keys causing your application windows to hide, rearrange, disappear off into other “spaces” etc etc
I always recommend FCP users remap Expose/Spaces/Dashboard to less obtrusive keys, as the default settings tend to clash with primary FCP edit keys
you can remap your keys in the OS System Preferences >> Expose & Spaces pane
if necessary, you can also disable “spaces” there too