As the creator of this thread, I really need to clarify:
The thread title is a bit misleading.
DNS-323 is fully capable of serving MKV files through SAMBA. That is, you can playback MKV files from your computer without any problems. As far as I know, this applies to firmware versions greater than or equal to 1.07.
The MKV streaming problem exists only as far as the UPnP AV Server is concerned. In other words, the DNS-323 will not serve MKV files to your tv box, for example. As posted in this thread, a simple solution is to rename your .MKV files to .MP4.
Apart from that, I believe there is no other playback problem with MKV files stored in the NAS and accessed by a PC via a mapped drive, a network share etc.