You can also use ClownBD to convert an mkv to Bluray structure: it's a GUI front-end to eac3to (for audio and demuxing), BDsup2sub (for subtitles) and TsMuxer (for muxing) used in the process.
For anyone interested, there are a couple of programs called easySUP/goSUP that can convert srt subtitles into Bluray compatible PGS form. I also recall there being another utility that can force subtitles in Bluray structure, although I can't remember what it is called.