I am have a few problems with my mkv conversions. I have a couple of dual audio mkv in which english is not the default language. I want to put these on my Ipod however all the programs I have to convert to mp4 use the default stream only (tmpege, Super). I have tried to use mkvmerge but when I remove the first stream and leave the second, I get audio pin error for Vorbis when I try to play it back. I have coreVorbis, and I can even extract the .ogg audio and play it fine. Problem only happens when I try to remerge the mkv with just the second audio stream. I have also tried using Super and telling it to use Stream #2, however this disables Directshow filter and my video gets cut. Its not dropping frames because it doesn't go through the entire video and the audio is in sync the entire time. It just seems to remove half the clip entierly (I also had this problem with mkvtoonnix when I am not even reencoding the video, just repacking it). I have no idea why it is doing this. The frame rate before and after encoding is 29.93. My final option I tried extracing the second audio stream and the video seperatly then combining them. This kept the origianl length, however the audio doesn't get extract correctly and when remerged is very off sync because it cuts audio when extracted. So my question is, any idea on why its cutting the video (even when its not reencoding), or why I would get this audio pin error (MPC) for Vorbis when I clearly have the codecs to play it (as I can extract it just fine). Or better yet a free program that will allow me to choose which audio stream I want when I encode? Thanks!
Should also add it is only cutting the video in Super when I deselect Directshow filter. If I leave it checked, the video encodes fine, I just can't change the audio then.
