I dont usually play mkvs becuase I have notice a loss in picture and audio quality when playing the files. Didnt do any tests to prove this but thats how it looks and sounds to me.
I figured out what the problem was. I had been using version 2.4.7 of mkv2vob and had been able to rip these files to play the DTS tracks via my PS3 and Onkyo amp. However, I also had "automatic updates" selected on the options tab and it had updated to version 2.4.9 which allows you to circumvent the Cine protection on these files but in doing so the DTS track gets replaced with a Dolby 5.1 track.
So if you have any type of modern amp which can decode DTS etc and want to hear the DTS track on Cine protected files, select the "Linear PCM option" on mkv2vob and stream this file to your ps3 and amp and you'll be able to circumvent the Cine protection as the processing is done on your amp and not on the ps3.