With one pass, it also stops half way in that pass with the same message.

When converting .mkv files with MP3 or AAC audio, it converts without any issues. That observation and the error message stating that there are too many audio packets in the buffer led me to I believe the problem is with Vorbis audio. So, I demuxed the problematic .mkv file, converted the Vorbis audio to MP3 with Audacity, remuxed the file as a .mkv container, and ran the converter and it came out fine. Another thing I noticed when running Vorbis audio in the converter is that the console notes that it is constantly dropping frames.

EDIT: I also wanted to add that I noticed that the converter was also dropping a lot of frames for .mkv files that have more than one audio track. In the case that I noticed this, the file has two AAC audio tracks. Demuxing the video (which was H.264) and one of the audio tracks and remuxing them fixed the problem. However, I would prefer not having to create an intermediate file to run the converter. Or at the very least, I would rather not have to remux the streams.