God, how can this be so hard? After wasting hours trying to google a way to set, using Windows software, the audio delay in an MPEG stream when muxing .m1v with .mp2 files, I finally came up with the following solution: download mp3DirectCut, then insert, or actually, copy and paste (as even with this software I wasn’t able to find a way to insert silence into the stream) the amount of delay of audio data into the beginning. Save and multiplex the new audio stream with your video. Enjoy the now non-displaced audio track.
Good Noodles.