bingo, what I was going to say.i'm sure there's a better way. i use mkvmerge to convert mkv to mka files then use quicktime to convert mka files to mp4 format.
dvd catalyst...takes mkv convert to mp4 format (droid option). i've converted many anime mkv files already. the subs and video looks great. i just happen to convert Bleach - Fade to Black...the other day and it superb :icon_ banana: