Audio problems converting AVi files

Sorry if this topic has been done to death elsewhere but I am having issue converting AVi files for viewing on an AppleTV 2. Although the picture quality seems fine, I get random but very loud clicks on the audio track. These happen sporadically but frequently enough to mean that watching movies/programs is not enjoyable. I have tried re-playing the affected files and the clicks and pops happen at the same points each time, meaning it does not seem to be a network or Apple TV issue.

Anyone have any suggestions for resolving the issue?

which import method and conversion tool are you using?