I'm also trying to use Handbrake to make an .m4v with subtitles burned in but it's grayed out I didn't check all of them, but the ones I have seem to have the same boxes checked in regards to audio & subtitles. So I want to make sure I'm choosing the correct file in Make MKV before problem solving in Handbrake. I've done this with DVDs no problem.
Does anyone have any ideas what's going on?