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7020100
(Get the code!)
This happens when running xmodmap manually or letting Gnome run it. But I think Compiz (and Unity) loads before Gnome.
I tested this by setting Ctrl+space to summon Unity and logging in again. Then I changed the summon key to Super and my remapped Alt still functioned normally. I verified this by leaving it set to Super, logging in again, verified that Alt was broken, then ran unity --replace. Since xmodmap had already run and now Unity was running after it, the remapped keys all do what they are supposed to do.
I.e. xmodmap after Unity will keep some holds on Super. I guess that Unity installs a hook on Super before Gnome/xmodmap gets a chance to remap it.
Should this be assigned to Compiz, since Unity is not the only keymapping that Compiz manages?
(Could this have been the reason why Gnome loaded the xmodmap before anything else, so that the user-defined keyboard shortcuts would be relative to any remapped keys?)