I bought a release of this four years ago at Sam's and it's in sync. Can't speak to the new one.
Have you tried playing it on a different DVD player to see how the sync holds? Stranger things have been known to happen. All DVD players (and DVDs) are not created equally. Probably won't make a difference but who knows.
I've watched the new WB version all through the holidays and I even just double checked it and mine is not out of sync at all. Not even a little bit. So perhaps there are bad copies floating around out there. I bought mine as an individual release, not in the the holiday box set.
I saw this yesterday after watching this DVD a few days ago, and just wanted to say its not the case with my standalone copy. I almost didn't buy it since I had the DVD release from several years back, but loved the special so much that I wanted to see how well of a job they did with remastering it and creating the bonus content.
I was impressed watching this recent rerelease the other night with just how well the original creators matched the movement of the mouths with what the characters were saying, so safe to say everything was in synch on my copy. I wasn't disappointed, besides being surprised they didn't show the Coca-Cola portion of the original introduction when they were talking about it on the interview bonus.
Its worth noting that it might be a sign your DVD player is going up. Mine had problems for quite a while with transitioning between scenes and such, sometimes causing the audio to become out of synch with the video. Finally, it started outright freezing and such, so I replaced it. Slim chance it might be that, though you'd probably wouldn't be posting since you'd of figured it out with it happening in other DVD's.
Perhaps the standalone release is different? I think it came out later than the bundled version, I think the bundle came out back in October when they released the standalone copy of "It's The Great Pumpkin, Charlie Brown'. So perhaps those of us with the standalone copies have the fixed version?
Just checked my copy (got it in the box set) and everything seems to be alright. There were a few points that seemed a bit "off" (the hello into the mailbox), but that was no doubt due to the animation at the time; and when compared with the original DVD appeared to be the exact same...