I have a large MKV with soft subtitles and 3 audio tracks. I want to convert to mp4 with burned in subs. According to Handbrake developers in this older thread, Handbrake only supports burning in subs on DVD sources which is why the box is greyed out (?) http://forum.handbrake.fr/viewtopic.php?f=11&t=15496 This movie was never a DVD. I tried it anyway with checking the other boxes and playing around with the formats and it still doesn't work with the subs. On MKVTools the subs show up, but it messes up the audio and I only hear it through one speaker. What should I use instead?