What's happening is that the DTS audio is being transcoded to another audio stream which can be output to your amplituner. If you check your audio output options in your PS3, you will probably find that DTS isn't able to be used (best if you go with the automatic settings since anything connected should tell whether it can handle it). Since it's not being used, it is transcoded to some other steam like AAC or the like which does work. Since your PS3 lacks the ability to transcode for itself, disabling DTS is the only way to get the audio to play.
Now, if you DO have DTS capability on your amplituner or whatever you call it, you'll need to enable DTS specifically and ensure the connections are the correct ones for DTS use. On top of that, you'll need to update the outdated PS3.conf file in the PMS program folder to output the DTS audio stream with whatever mkv is being transcoded as or it will be transcoded regardless of what checkboxes you have checked in your program. It will most likely be the mp4, but you should be able to tell from the file information in the PS3 triangle menu.