I have exactly the same problem with Videopad, version 7.3, after capturing video from DV-cam cassettes with Windows Moviemaker with result a DV-Avi file.
Videopad asks at adding of this file for choice of audiostream, no. 1 or no. 2.
Regardless of choice the result after a long adding time is one videostream and one audiostream, the audiostream being timewise much shorter than the videostream and much distorted.
I have been using DV-date for many years with good result.
Which conversion in DV-Date did you use?