So when you say "all of a sudden" you mean you logged in one morning and it didn't work? Or you added a new spell to your bar which uses a modifier key? Or you were playing around in ISBoxer one night while you were a little intoxicated and thought you had come up with a great idea? Or anything else that might have changed even in the slightest?

When you switch windows does the new 'master' get assisted by the others? If this is only happening on certain windows then your bindings are conflicting with the FTL modifiers.