Just picked up Wall-E...title 39 seems to be in the correct order on my DVD (single disc version). I could extract this using Handbrake, but had the same audio shift problem. To fix the audio, try extracting the video track, removing ~40 frames from the front (hold down shift and click right arrow 40 times, then cut), and "Add to Movie" the video back to the original file.
I noticed when playing the DVD on the computer, that if you manually rewind to the start, the movie will not play unless you fast forward it 1 second or so - my guess is that this is the audio shift problem.
My preference is to buy the DVD, make a copy for iTunes/Apple TV, then put the DVD back into the case and into storage. They sure make it a PITA. I am curious about the 3 disc version with an iTunes copy - what's the quality like?
Wait, what program did you use to "extract" the video and delete the 40 frames? Can you do that in handbrake?