Unfortunately certain files can have aysnc problems when transcoded, some of which can be fixed with normal settings or expert settings in PMS, and others not. If you need assistance figuring out what to do with a specific file, follow the Problem Reporting Guidelines
. Unfortunately fixing asynchronous playback is not my area of expertise, so you'll need a dev or another forum member to assist you.
As for the sound quality, yes it makes a difference, but there are plenty of other factors at play too (receiver quality, speaker quality, room dynamics, personal hearing, etc). It's a fairly subjective thing that you'll need to determine for yourself. Why not reencode a video, and then do a blind test to see if you can pick the difference between the source and the reencode?