This is very strange indeed. You mentioned to me that you ripped the AC3 from my ESB AVCHD and it synced up perfectly to your video. Well i didn't have to change the speed of the audio to sync with the video so it is the same speed and pitch that it was ripped from the laserdisc

If you have sony vegas you could try loading your video and the downconverted wav files into that to see if they sync that way

You're not joining the 3 AC3 files together and trying to sync the whole file that way are you?