I understand the desire to get it for free when converting, I really do. But you often get what you pay for. I had a horrid time using AVconverter (in all it's versions) on my work laptop. Compression looked bad, video never right, and so on.
Using my Mac at home, I had no issues, as I have a decent converter that I purchased. But I wanted to find a better option for the PC. Preferably one that could be used on both platforms.
So I tried the one from here:
http://www.mp4converter.net/
Available for both PC and OS X. Works like a champ. I just chose a custom setting, entered the parameters my player needed (bitrates, fps, size, etc.) and it worked the first time. Granted, I was looking for something that could handle several different formats for various players and computer devices, so I needed something more than a basic converter.
You can get a free trial to see if you need something that has more bells and whistles. I'm not telling anyone to stop doing what they are doing, nor am I making a penny from my personal recommendation. I just wanted to put an alternative out there for folks who are having issues with this particula bit of software.
I've also had success using some of the graphical front ends that use the ffmpeg code for conversions. Haven't had a sync issue with any of them.