You are right, I just updated the svn copy to the latest and compiled, now the audio really does work!
I do, however, have still few problems: on most of the mkv's I cannot get subtitles working, and with many of the mkv's I get ffmpeg errors in log (some of the errors don't seem to have any effect on playback, some will prevent it), but I guess those might not be related to this issue.
Anyway, this is great news, it's been a while since I could actually use ps3mediaserver
Ok just tried with a mencoder-mt compiled from svn revision 29544 and guess what ? It works !!
The mplayer team has corrected this annoying bug in the latest revisions, and now all workd perfectly.
So if you have problem, just get a svn version of mplayer and it should do it.