Whenever audio is giving me trouble I extract it as a WAV file using VirtualDub (e.g. 'audio.wav'), then create a batch file ('audio.bat') with the 'BeSweet' command line shown below and then run the BAT file to create a clean 'MP2' file with the required conversions. I then merge this with the video file using the TMPGenc 'MPEG Tools'.
BAT file command:
Code:
"E:\Program Files\BeSweet\BeSweet.exe" -core( -input d:\audio.wav -output d:\audio.mp2 -logfile d:\audio.log ) -ota( -g max ) -ssrc( --rate 44100 ) -2lame( -e -b 224 -m s )
The '44100' is the output frequency you want and the '224' is the output bit rate (you can change these to anything you need).
This seems to cleanup most audio problems, however if it's a frame rate conversion problem (e.g. from a 30fps capture to a 29.97fps encode) I use Avisynth scripts to frameserve with video/audio framerate conversion with forced audio sync enabled).