REcontaining video from MKV to MP4

[Artemicon]

So I've been having a rather annoying problem that only happens every so often and I'm looking for some more knowledgeable people to shed some light on this subject for me.

I've been converting all of my .mkv files to .mp4 for watching on my apple tv and for the sake of simplicity and time I've been extracting the raw video/audio/subtitle files using MKVExtract and then using MP4BoxGUI to remux the raw files into a .mp4. This has been working spectacularly with the exception of a couple of movies. When I remux those movie files using the exact same method to convert hundereds of other files those few files have seen the audio go offsync in excess of a couple of seconds, and I might be losing my mind but the further the video goes it seems the audio is even further off than what it began to be.

I was wondering if anyone has encountered this before or knows of some other kind of software that is better at remuxing raw files into .mp4 than MP4box.

Thanks so much for the help!

[hey]

Just a guess, but is the video vfr?

[Boyiee]

I convert a ton of movies from all types of shit to mp4 using handbrake for my dad's apple TV 3. never had any problems at all except with 2 file movies, cause I'm terrible at merging them into one, and I've never tried writing the subtitles to them.

Handbrake is great but I have never tried Subtitles.

it's extremely easy if you don't want to use subtitles or multi file movies. select file, select output type, click apple TV 3 setting, press start.

[Artemicon]

The videos are not VFR.

I don't want to re-encode the video as that takes 20-30 minutes a video where as re containing them takes less than a minute. Its not subtitles that are off they are where they should be in reference to the video, its the audio that is behind the video.

Thanks for the suggestions though.