Take "Flatten image". One can be in layers menu and assign a shortcut for
it there. That shortcut will not be assigned in image window. 

This may be not a bug, but I don't expect somebody to have different
shortcuts for Flatten image depending on which window (layers or image
window) are active. I'd rather expect that assigning a shortcut in one
place would be transfered to all gimp windows. 

mimooh