Ok, I think I found out where the problem is. It seems it's related to
the option to disable the screensaver.

If you turn off the option "Disable screensaver" (under
Preferences->General->Video) the problem doesn't happen.

When that option is on, smplayer passes to mplayer the option -stop-
xscreensaver, and I guess mplayer moves the mouse cursor from time to
time to avoid the screensaver to turn on. And smplayer detects that move
and shows the cursor...

This actually seems to be a bug in the karmic package of mplayer. I guess that 
package is patched to support the gnome screensaver. The problem doesn't happen 
with my own build of mplayer that you can find here:
https://launchpad.net/~rvm/+archive/mplayer

So summing up, this is not a bug in smplayer.

-- 
A mouse pointer keeps reappearing during video playback in smplayer
https://bugs.launchpad.net/bugs/455073
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