Handbrake alternative with non-dvd subtitle support

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?

But subler only adds the subs like I could select them on a compatible player, right? I want the subs burned into the video so they're always on.

I'll try that, thanks.

In subler, the subs are apparently in substation alpha format. If I can convert it to srt, I can prob do this all within handbrake.

Very annoying there's no all-in-one app for this. Roadmovie looks like it would be except it's not showing the subs >__<

Last resort is sending this to my vmware vm and doing it through mkv2vob