How did you enable mkv playback in wmc? How do you have your codecs setup? You aren't always going to get FF and RW to work out of the box even with codec packs. I had really tweak my codecs to get FF and RW working g BUT skip ahead and instant reply are much easier. I have seen Incorrect codec configurations act like network issues.
I was using MPC-HC previously which has LAV Codecs.
I also have LAV Codecs installed for when I use the internal player.
If there is particular settings that I need to take into account then please advise.