K, I'm mapping super+2 to launch Terminal. When I enter it into the GUI, I get "<Mod4><Super>2" listed in the treeview. However, when I press the key, nothing is launched (though it appears to be grabbed). Added printf() in _handle_key_press(), and gtk_accelerator_name() is returning "<Mod4>2". My xmodmap says: shift Shift_L (0x32), Shift_R (0x3e) lock Caps_Lock (0x42) control Control_L (0x25), Control_R (0x6d), Control_R (0x6c) mod1 Alt_L (0x73), Alt_L (0x7d), Alt_R (0x71), Meta_L (0x9c) mod2 Num_Lock (0x4d) mod3 mod4 Super_L (0x40), Super_L (0x7f), Hyper_L (0x80) mod5 F16 (0x5d), ISO_Level3_Shift (0x7c) Clearing out mod4 and then attempting to re-set the shortcut in the GUI doesn't change anything (it still shows "<Mod4><Super>2").
This is a duplicate of bug 4304.
I can also confirm this problem. For me working shortcuts depend on the Num Lock key, somehow. *** This bug has been marked as a duplicate of bug 4304 ***