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I just had to notice that recently the altgr key (right apple button) on my iBook does not work in GTK apps. But it does in QT ones. Of course. ;-)
Though this time it was not a GTK bug but an xorg one.
Now that these days we have git bisect, it was trivial to find the bad commit, though to make bug-hunting still fun, there were numerous xorg modules to poke before I finally figured out this will be an xkeyboard-config bug.