Hey there Rodoga,
I ran through what you suggested for doing this all from the command line and it worked AWESOME for my 29.970 frame rate mkv files but for my 23.976 mkvs it seems to only encode the audio and ignore the video, even though Mediainfo says that the video is there and at the correct frame rate...
Any idea why I'm running into this and what might solve it? It's very consistant.
Thanks again for your awesome command line based solution!!! I plan on wrapping it into a perl script so that I can have it run through a whole directory worth of stuff.
On a slightly different not a guy named darick created this gui wrapper for the same process you created called Video Encoder, as seen here: http://videoencoder.codeplex.com/
It too works GREAT for someone that doesn't want to mess with the command line. Unfortunately for me it has the same results as your command line batch file.
Any ideas would be very welcome, thanks again!