AH, that is definitely a horse of a different color.
That is a Gnome 3 default key combination for window switching.
Try this: Change 'Key to flip through windows' in the switcher from disabled to something else.
I pulled that out of an Ubuntu/Unity how-to and I am in the 12.04 OS right now so I can't test it out for you. But what it boils down to is that the alt+` key combination is a default setting, so by changing the combination for flipping through windows to something other than 'disabled' which means (to Gnome 3) default setting, then you should be able to stop the window manager from responding to that key combination.ref 1