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As you suspect the kernel is one place to look into
It could also be how your xorg.conf is setup - have you got any chance to compare?

he problem is the same in consolle mode, so I think is not related to Xorg.conf.

Yes if you mean a "real TTY" not gnome terminal
Sorry - but I'm clueless
The risk of things like that is why we want to limit the possibilities to update...