I thought it would do the trick, but at this point it's not doing the trick because it's not free! Seeing as I only need it just for this one thing I can't justify the expense.
Until recently I had been able to use Quicktime 7 to perform a passthrough encode of MKV to MP4. Meaning there is no need to re-encode audio/video. This means you can convert an hour long MKV file via pass through encode to MP4 in about 30 seconds to a minute instead of having to use something like ...