i'm not quite sure what you have converted to what exactly. i thought you were going to use autoGK to convert the dvd files to avi, since the mpeg was poor and only half of it was converted.
what do you want to do with the WMV file?
dvdsanta can convert WMV files to dvd format, but i don't think that is what you want to do. does virtualdub not open the WMV file?