VirtualDub allows you to adjust the video stream's frame rate so the video and audio durations match. This probably isn't what you're looking for, but it might be interesting to try it and see if it puts everything back in sync.

Video menu --> Frame Rate --> "Change so video and audio durations match"

By the way, at any time in the process did you compress the audio? In some editing situations, that might cause desynchronization issues.

-- Little_Dragon (Animator #11.3)