[Kayley Grace] "The issue seems to be when the imported video is a wmv."
I've experienced something similar myself and verified it for a poster on the SCS forum. Encoding WMV (you don't "render" WMV, you encode it) always results in an audio track different in length from the video track. (I tested it in V10) But, since I've never had a client ask for WMV files, it's never been a problem.
Steve Mann
MannMade Digital Video
http://www.mmdv.com