Wow, that's a lot of links
I did some research too & managed to convert a couple of videos with no audio problems. The audio settings I used:
Bitrate - 128kbps
Channels - stereo
Sample Rate - Input (default)
Volume - 100%
*Also converted one file at 200% volume but it made no difference to the volume when playing the video in iPod. So da1nonly's settings were right for me!