I've just setup a new NAS server with FreeNAS running and MiniDLNA as a plugin.
And as a player I'm using Samsung BD-E5300 Blu-Ray player.
Seems that it's impossible to get the external subtitles working for MKV's or AVI's via dlna.
Embedded subtitles works just fine in MKV files.
My friend has a exactly same kind of setup as NAS server, but he's using Samsung TV as a player and subtitles works just fine.
Hope that I can get some kind of support and solution from here to get my system working properly.