OK, I have searched more for the problem. Firstly here is the original file:
https://rapidshare.com/files/2599197155/Pana8hnaikos.vs.Do3a.Dramas.B.hmixrono.mkv
I want 1 fragment from 00:42:56:968 to 00:44:55:314. I tried cutting that on my Windows 7 PC with K-Lite Mega Codec Pack 8.2.0
https://rapidshare.com/files/3920192443/Pana8hnaikos.vs.Do3a.Dramas.B.hmixrono_Trimmed_7.mkv
and if I play it
with VLC it stops at 1:29 of the total 2:03 of the trimmed file
BUT with the MPC bundled with K-Litethe file sound plays correctly from 1:29 and beyond.
I have a virtual machine with VMware that have Windows XP on it. I tried the same procedure
https://rapidshare.com/files/1361202572/Pana8hnaikos.vs.Do3a.Dramas.B.hmixrono_Trimmed_XP.mkv
and the sound on the output file played correctly both on VLC and MPC!
So something goes wrong with VLC on Windows 7 or something only on my PC
I use only RapidShare after the MegaUpload fiasco when I lost 200GB of uploaded sport retro videos.