Ok, a last for tonight

, I think this one is not related, even if the symptoms are similar: The movie start correctly, and after maybe 10s it stops and the screen keeps black forever....
I think here it is linked to an mencoder error, and I know that the mkv file is corrupted (limited to 4Gb, the end was dropped).
However, mplayer is able to play the "amputated" mkv, so I hoped that the transcode would have worked, except maybe for the last minutes or so...
mplayer is not able to jump around the file, though, except if I add the -idx option...which is common on partial files without the end section...I do not know well mencoder, but maybe there is a similar option (i.e. "-idx"), to ask to regenerate the missing file index, that could help?
Hehe, indeed, adding -idx in the custom option of Mencoder (to force it to rebuild the index, if it is missing), helpsed! restarting PMS, now my partial mkv file play nicely

OK, I will try the other file which was blank, to check if it help, but it is, I think, a valuable trick already, maybe this option should be activated by default?
Bingo, the previously black movie now run!!!!! there is still a sound/video synchro issue, but I will try to solve it, I guess playing with other Mencoder options may do it...
Great, I hope this solution (add -idx in the Transcode settings/Video files engines/Mencoder/custom options ) will help others too

I still add the debug.tgz of the partial mkv file, that played for 5s before going black without the -idx option, for the record