What's the bitrate/size of the MKVs? It sounds like your network should be good, so my best guess is you're hitting the software bitrate limit on the 360 if these are 1080p files that are not heavily compressed.
It's been over a year since I was doing the 360 WMC extender thing, and I never did dabble with MKVs. All my movies were ripped to 1080p h264 with DD audio. I tried both .m2ts and .wtv containers because they are "natively" supported in Win7 and the 360 extender.
Depending on the size of the file, I would hit this software limit and get stuttering with certain files in an .m2ts container. If I remuxed the same file into a .wtv container, no change to the video or audio, it would play back perfectly.
I'm guessing your MKVs are behaving the way .m2ts was for me. You should try converting one of your problem MKVs to .wtv and see how it plays.
It's pretty stupid and would suck if that is your issue, because I would not recommend converting all you MKVs to WTV. Unless you are really sold on using 360s as extenders.