This happens reliably with xserver-xorg-core 2:1.4.1~git20080131-1 and xserver-xorg-input-kbd 1:1.2.2-3 here as well - If a metacity shortcut involving ctrl and alt (no others were tested, but probably have similar results) is held until the key would normally repeat, ctrl and alt are permanently on until the server is restarted as far as metacity and xkbwatch are concerned, but work normally in xterms.
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