I have found that the easiest thing to do with large mkv files that wont fit on a DVD or a FAT32 drive is.
1) remux them to mpg with mkv2vob
2) include in the media server share
3) either play remotely or copy onto the PS3 via the media server.
Copying onto the PS3 also has the benefit of fixing any problems with network congestion or wifi not being able to keep up. It will also rectify any problems caused by fragmentation of the remote file as it will probably not be fragmented on the PS3.