I recommend Plex (I know I know, I read the question)
I have an Ubuntu 12.04 box running that.
Don't generally have any problems with it.
I did have an MKV problem where some encoding option caused it to barf but that was with DLNA clients and the transcoder.
And it does have the advantage that you can get paid support for it at a very reasonable price.
The MKV files that are missing, are they missing on the PMS or just missing in the client?
And is the client DLNA or the native Plex client?
Also, if you have a Samsung smart device you can install the native plex client on there.
I have also had success with the following servers:
miniDLNA (only used for music on an RPi on a boat though)
Serviio (superior DLNA transcoding)
XBMCs built in server (seems to work well)