Comment 11 for bug 568401

After digging further into the code, I found the problem: the egg_keymap_resolve_virtual_modifiers() function in indicator-applet-0.3.6/src/eggaccelerators.c returns concrete_mods=0 for modifiers that are not bound to any key (which I confirm happens for Super key in remote session).
As a temporary (?) solution, I propose not to grab a key in indicator-applet-0.3.6/src/tomboykeybinder.c:do_grab_key() function if binding->modifiers equals zero.