I found that VLC cannot synchronize correctly with mkv/oggTheora files.
for example, there's a mkv file has such structure:
Track 0: |========[Video]========|
Track 1: |[Silent]===[Audio]========|
Track 2: |========[Subtitle]=======|
VLC will ignore the silent audio and all other tracks are cropped also:
Track 0: |===[Video]========|
Track 1: |===[Audio]========|
Track 2: |===[Subtitle]=======|