It seems to be solved with a new version of MPlayer.
This is very strange however, because MPlayer was not the problem.
Now the video plays smoothly with loop filter enabled, 2 threads, and MPlayer v. 31027 (p4 multithreading) taken from here:
http://oss.netfarm.it/mplayer-win32.phpLet me know if I can help finding the problem with the MPlayer version SMPlayer 0.6.9 comes shipped with, because since MPlayer isn't the problem (though, strangely, I solved it updating it), this could happen again with future releases.