I have been experiencing the same issue with this command with the current
version from testing (1:3.20140805.1-2). I fixed it for myself by reverting to
the version from stable.

In my case issue manifests from this use...

$ xdotool search --class URxvt key --window %@ "Ctrl+Alt+0"

Ctrl+Alt+0 changes the font size via a XResources binding on urxvt. The
terminals all receive the "0" without the modifiers.

-- 

John Eikenberry
[ j...@zhar.net - http://zhar.net ]
[ PGP public key @ http://zhar.net/jae_at_zhar_net.gpg ]
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