I’m an old fart, and getting lazy.
Luckey, Sagi-good friend and creator of the extremely handy- "ER Media Toolkit" has explained this in detail in the ER Media Toolkit User Manual.
I hope Sagi doesn’t mind that I copy/paste this part here.
About the option "Auto Fix Offset Issue"
Auto fix audio offset issue’ (enabled by default). Introduction and background: Due to extensive video decoding time some highly compressed and complexed codecs are designed to offset their included audio streams to ‘force’ video audio playback synchronization while played in their native form through various media players in various devices, However, converting those codecs into none compressed form may introduce the opposite result! Therefore, we designed a unique smart algorithm that detects those potential offset problems in both input and target audio/video and only if necessary adjust intelligently the audio stream offset to keep it ‘in sync’ with the target video, resulting in less than 1ms (less than 45 samples) sync accuracy between video and audio streams with most popular mp4 but never ever risking adjusting into negative values that result in audio material beginning cutoffs (as you may experience with most other conversion algorithms that try to deal with that issue). This fix applies to AAC and MP3 audio streams, all other codecs unaffected in this process. If you choose to disable this option the audio will not be analyzed and processed with this unique algorithm and shall be passed on exactly as it originally created in the source media (this method is unique for ER Media ToolKit in both Video and Audio conversion or ‘Extract Audio to Wave’)
Do yourself a favor and download ER Media Toolkit and donate.