What's the Best MKV-to-MP4 re-coder (NOT en-coder)?

[Rumourd]

I've been trying to change my MKV files' containers (of HD content) into MP4 containers, using ShanaEncoder's "Stream to Copy MP4" preset. So I'm clear, I am NOT looking to convert them using HandBrake -- no conversion wanted or needed. I want an exact file size duplicate, only in the MP4 format, for when I travel to a friend's place that can't play MKV.

So, the new MP4s get created 1:1...

The files play fine in VLC. But when playing said MP4 files (anywhere from 2-10GB) on my Sony Blu-Ray Player from a USB 3.0 flash drive, their playback is stuttery, as if ShanaEncoder grabbed a wrong pulldown frame to begin encoding. However, both the player and flash drive WILL play the original MKV just fine, regardless of file size.

I also don't like that ShanaEncoder won't allow you to convert different audio streams separately -- for instance, I want to convert an MKV's DTS streams to AAC...but I want to passthru the AC3 streams as they are (no conversion). With ShanaEncoder, it gives you only ONE conversion setting which affects ALL audio streams. Also, there
seems to be no way to burn-in subtitles for foreign films. And we all know how troublesome MP4 is with subtitles...

Anyway, Handbrake handily handles the subtitle burn-in and the separate audio stream reconversion...but it cannot simply RE-code an MKV to MP4 without a conversion.

So, what're some other programs that can do MKV--->MP4 container changes?

[sneaker]

ffmpeg (and many GUIs based on it like e.g. X Media Recode)
MkvToMp4 (not updated anymore, unfortunately)

[video.baba]

You can always try my program, BOX4, to see if that helps but I would like to draw your attention to one thing.

Also, there seems to be no way to burn-in subtitles for foreign films. And we all know how troublesome MP4 is with subtitles...

You can not do this with any program, now or in the future, without re-encoding the video.

[netmask56]

You cannot burn in subtitles without re-encoding the video as the burn in process is changing the video. The best you could do is add the subs to either a MKV or MP4 container and make the flags for the subs both forced and default and hope you player respects them. So to burn in means to reprocess the images that make up the video content.