I have come across more and more movies that play fine with VLC on my mac, but claim to be corrupted when transcoding to my PS3. In every case, extracting the audio and video tracks with MKVtools, then remuxing the tracks back into an MKV with MKVtoolnix, has fixed the movie. My new muxed file plays fine. Doesn't take too long either. Perhaps 10 min to extract the files, and 3 min to remux.
P.s. when remuxing with MKVtoolnix, be sure to set your framerate for the video track to what the movie originally was, or your audio and video will lose sync. In 90% of the cases, this is 23.976