Megui Auto-Encode MP4 container

[ZenMystic]

When I manually encode video and audio separately by manually pressing the respective encode button, it will allow me to directly encode into either an MP4 container, MKV container, or raw. And then at the end of the encode, mux the video and audio together. when I use the auto-encode option, it only seems to encode the stream as a raw stream, and then naturally mux it into an MP4 container later.

My question is this: Is there a way using the auto-encode option to get Megui to encode it into an MP4??? and then naturally, later on to mux the MP4 files into a... say... MP4 container?....

The reason why I ask this is because my encoding is going fine... but when it comes to muxing, unless it's an MP4 stream, I am finding that MP4 box is not muxing the files properly, for example: it seems to have issues muxing raw streams, but I'm not having the same issues and everything works fine if I mux MP4 streams into an MP4 container. Anyone else having this kind of issue?

[ZenMystic]

UPDATE: I can definitively confirm it is the muxing process that is giving me issues. Having the video or audio in it's own MP4 container by itself everything plays fine. however, when I mux the two streams together with MP4 box, that is when I get the issue of 'stuttering' in the video. this is not an isolated incident. it's happening with every single file I mux together. is there any other software other than MP4 box I can use to mux streams into an MP4 container? I did not seem to have this issue years ago with MP4 box when I used it. However I cannot recall what version of MP4 box I actually used.

[D_Knife]

You could get MeGui to mux into MKV and mux into MP4 later...