I would suggest adding:
http-get::audio/x-matroska:,
to protocolinfo.txt. BubbleUPNP will send this as the content type (when using it's internal/local media server) for .mka audio files. (In my case, it was multi-channel audio ripped from a bluray and encoded in a matroska container.)
Recent versions of mpd appear to have no issue handling it. You might want to also add the non-x variant as well for completeness, but I'm unaware of any clients that send that.