Okay, something seems to be wrong with the aac audio inside the file or how I handle it since, mp4box&mkvmerge crash on it but when I reencode the stream everything works like it should.
Okay, mp4box provides some info: "Audio isn't MPEG-2/4 AAC with ADTS"
Seems like I got a bug when passing through aac audio -> will try to fix it
Found the bug and a fix will upload a fixed version.
Cu Selur