Use remux instead (http://www.macupdate.com/app/mac/35968/remux). It too is free, and it works the same way — by re-multiplexing an MKV's video, audio and subtitle streams into a new container (e.g. MP4) without re-encoding — therefore it’s LOSSLESS (zero quality loss) and takes just seconds or minutes instead of hours. However, MKV2PS3 can only remux .mkv files to .mp4, while remux can re-multiplex TO and FROM .mkv, .mp4, .m4v, .avi, .ts and .vob.
MKV2PS3 can convert a video file’s DTS audio stream to the AC3 codec so it’ll play on PS3 or AppleTV (both of which require either AC3 or AAC), and it can convert 5.1 Surround AC3 audio to stereo, but it offers no bitrate control. Remux can do the same things but more flexibly, plus it allows you to convert to the AAC audio codec (2-ch. or 6-ch. 128k) that many people consider superior (especially for stereo audio streams and lower bitrates), and it gives you two AC3 bitrate choices — 448k or 640k.
Furthermore, MKV2PS3 “doesn't produce strictly standard conformant MP4 files,” while remux does. This means that videos converted with MKV2PS3 won’t play “with the default video player iOS-based devices (iPhone/iPad),” but vids converted with remux will.
Lastly, the documentation’s statement that “MKV2PS3 is distributed as a free public beta at this time” gives me the impression that its freeware status is only temporary. I could be wrong, but I suspect we’ll have to pay for this app once they’ve worked out all the bugs. Remux has been out of beta and free for years.
BTW, I don’t know or work for remux’s developer. I’m just a big fan of great freeware video apps, especially since there are so few of them.