It came to light, that problem still remains, so I attached a number of files 
from troubleshooting wiki you pointed.
1) Gnome-settings-daemon, gnome-power-manager and any keybindings make no sense 
at all.
2) The keys like Alt+F1 work well in X (as I said in the bug description), but 
are also somehow passed to "underlying" console (we remember, that exactly 
Alt+FX is used to switch ttys in console, instead of Ctrl+Alt+FX in X-server), 
so I suppose, any X programs don't have responsibility for this problem. The 
root of the problem, I suppose, should be found somewhere in gdm or plymouth, 
or something like this.
3) I've also found that problem disappears when I logout from the session. In 
fact, Alt+FX combination works well even in gdm after system startup, but when 
I logon and logout (AFAIK, X-server is restarted after that), everything is OK, 
both in gdm and in new user session. I think it confirms my suggestion in 2).

If you need any additional info, configs or anything else, feel free to
require :)

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Ctrl+Alt+FX hotkeys has turned into Alt+FX
https://bugs.launchpad.net/bugs/618665
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