First of all, thanks for PS3 Media Server, it's a great piece of software.
Now on to my "problem". I am trying to stream MKV with DTS to my PS3, and PS3MS transcodes the DTS audio stream into a low (350ish kbps) AC3 stream. I want to keep the DTS, since my A/V receiver is DTS compatible. On the other hand, this same file remuxed into VOB with MKV2VOB and with the DTS stream converted into AC3 has a 640ish kbps AC3 stream. Still I am grateful for being able to properly stream MKV files now, no stuttering, working like a charm. No need for me to remux them into VOBs any more.
I am using 1.04 on a heavily overclocked Q6600 over Gigabit.