Subler 0.9.3 is out. havent tried the mkv -> mp4 remuxing, but it sounds like it works.
http://forum.handbrake.fr/viewtopic.php?f=14&t=9197&start=150#p62545
If you have the newest VLC on your computer, Handbrake is fantastic at taking nearly anything playable on your Mac and converting it to your choice of codecs..