from an mkv. It's my understanding that handbrake doesn't recognize BR discs as a valid source. Has that changed with the nightly builds?
Not sure, as I never use it direct from disc. First, when you ripped to mkv (I assume using MakeMKV) you told it to included forced subs, right? If you did, open the mkv using VLC media player. FF till you get to a subtitle part (I like the one where she is in the sushi bar in Japan
). When you see the subtitles appear, check the subtitles menu (under video pull down, I think) and see which subtitle track is check. Make a note of it, then go to HB and open the mkv in HB. Go to the subtitle tab and select the track that you noted from VLC. If you want, just encode the chapter that your subtitle scene occurs in to make sure it is working. If you are getting it to appear, then go back and do the whole thing. It's a little quicker for these tricky things where you are testing various approaches.
Also, doing it this way, make sure "forced subtitles only" is NOT checked. It will discard it because the track is not flagged as forced.