In ubuntu 12.10 (unity) the option in smplayer to disable the screensaver no longer works at all. It works in gnome-mplayer 1.07 though.
smplayer should change to use this method to disable screensaver: https://bugzilla.gnome.org/show_bug.cgi?id=579430#c35
Should work in both gnome and kde, I think this is what gnome-mplayer now uses
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I've recently started testing ubuntu 13.04 and I noticed this problem doesn't seem to happen there :)
I can confirm that 12.04 LTS with the "LTS Hardware Enablement Stack" aka 12.04.2 backported from 12.10, also has the same bug :-(.
There is a new package - xserver-xorg-lts-raring. It is X from 13.04 ported to 12.04. It looks that everything back to normal.