can you play included subtiltes from mkv files? You should be able to verify it with mplayer classic or nfo file. You can also try example working on Samsung U40 something ... srt file attached to thread.
I am not sure if you need to change filename to same as video file but pls make sure you do it. Also make sure that you don't have extensions hidding in os or similiar stuff and use cifs to provide those file to video directory. I've experienced issue with db sync in twonky while I was adding files via ssh (It required to reboot nas to see it in media server in tv). Issues does not persist with Mijzelf entware mod, but was observed with FFP.
this will show subs in 0.64