MKV.. are you sure you have the Matroska plugin? http://matroska.org/
perhaps XBMC has difficulties to read them of to process them.. have you tried VLC to play the .mkv just to be sure it isn't a hardware problem?

If you have the Atheros Wireless Network Adapter, it may be worthwhile to upgrade the driver to 9.2.1.432 or later to eliminate the DPC Latency in the earlier driver versions. You could also download DPC Latency Checker to determine if other drivers on your system are causing latency.

Are you running the latest version of XBMC? It looks like you have some company in this stuttering issue with 720p .MKV files. 380mcn's idea to try another player is a good one (for troubleshooting's sake at least), although VLC also appears to have its share of people reporting this problem.

What Antivirus software are you running? Does disabling the Antivirus software Services and rebooting your system to unload the kernel mode driver(s) resolve the issue? If so, you could try excluding XBMC and the .MKV files from Antivirus scanning.

Since you report XBMC plays 1080p .MKV files perfectly, I'm suspicious that it is having trouble handling the 720p .MKV files and the above recommendations will have little if any effect.

OMG that Driver! If Asus would only update the driver on their support page, we'd have one third less cases. Lol