It has been my experience that using .mp4 is better than .avi. Typically, if and when I have to do any conversions, I use the Convert-It default settings.
If your source file is marginal or not within ideal spec, then you may run into sync and other issues.
Are experiencing this when using GameEx itself? If so, are you using LAV codec?
The link you have referenced is to someone's user profile post list. Please provide a new link to the post you were originally attempting to reference. Thank you.