After playing around with this and other converters, I've noticed few things. First off, .ogm files with DivX and XviD video and Vorbis audio go through the converter just fine.

Second is that I believe that the problem that I am having is an inherent problem with MEncoder. After trying out MediaCoder with one of the .mkv files I am having issues with, it too stopped approximately halfway through the conversion. A manual run of MEncoder via command line using the same file yields the same results.

So I suppose until the MPlayer team finds and fixes the problem with MEncoder, this problem isn't going to go away. So for now, I'm going to have to demux the Vorbis audio, convert it to MP3 or WAV, mux the video and new audio, and convert. What a pain.