I am newbie so I am just posting because others might have the same issue.
I used Makemkv to convert all my entire dvd library. 900+ dvds. (This does not include blueray. I am still having trouble with the audio sync with makemkv.) SO I was having trouble with the audio not syncing. My MKV file was perfect, but handbrake jacked it up some how. I read stuff about "muxing" but it was far too involved for what I was trying to accomplish. I had no desire to remixed 900 audio tracks. So I figued out if I leave my file in MKV format and not try to put them in mp4 format and set it for audio passthru my audio problems disappeared and handbrake became usefull.
Makemkv is very useful tool. I purchased it to show my gratitude to the programmers.