When I've done some slideshow movies in WMM in the past, there were some options of indexing the audio and video files and making sure they lined up correctly and how often the program would check it as it was being uploaded. I tried looking around for it on the capture end, but without a device connected it won't let me explore the options...

Anyway, see if you can somehow add indexing for it. I was also thinking that it could be a codec issue as well, do you know which ones you currently have installed for both the video and audio?