Comment 7 for bug 455073

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.