I am having the same issue with Kill Bill v1 that I was having with the Star Wars movies (those were fixed by this post http://www.makemkv.com/forum2/viewtopic ... 087#p16087). Kill Bill v1 has less than 6 English subtitles to pick from so I figured I would try every combination to get it to work thinking it was the same issue but after trying every combination I cannot get the English subtitles to appear for the Japanese conversations on any of them. They work fine when playing on a stand alone blu-ray player but not using makemkv to convert.
I can still rip them in a very time consuming process of actually playing on the blu-ray player, hdmi out into a hd fury3, then into a Hauppauge hd pvr to get it on the pc. This then captures the movie in a .ts format which I can then edit/convert to any format I want. I would just rather not have to spend several hours to do this when it is much easier and faster converting using mkv which I do for all my other dvds, blu-rays, and hd-dvds (about 75% of these as I have several that just won't work in makemkv or anything else other than a hd-player).