How to convert from MKV to MOV?

Hello, I have been having some problems with Xvid4PSP 6.0 lately. I convert TV show episodes mostly and movies from MKV to MOV and there are 2 files that Xvid4PSP 6.0 simply cannot convert. It stops randomly and freezes the encoding (not the program, though, just the encoding process) and then crashes when I try to abort it. This doesn't happen with all files, just 2 and I've looked at them, but they are the same as all the other files. Anyway, I was wondering if anyone knows what is up with this or maybe you can recommend me another (free) converter I can use? I've tried Format Factory but it is too slow, it takes me up to 3 hours per episode/movie and I need something faster, 10-20 minutes per episode (40 minute video) or less. And that doesn't leave a watermark at the middle of your video.
P.S. Please excuse my English, I'm not a native speaker.