My swaps are done using F1, F2, F3, F5 and F6 with the ctrl modifier. On swap, my personal TOGGLE-SLOT is called which calls jamba master in WoW keymap to self.

Now you have me wondering if one of these modifiers are falling through to the mapped keys and picking up shift + alt + F12 instead of ctrl + shift + F12. Though that doesn't sound right to me as jamba master to self only goes to the one window. Assuming strobe would have to be turned on all of them to do what they're doing?