I have a problem with the audio on one specific movie I'm converting

[JLW]

I convert my movies twice, once a smaller sized MP4 with AAC for all of the portable devices we all have (everyone in my house has an iPod, Zune or something else that plays MP4 video), and then in a larger M4V with AAC and AC3 audio for use with my AppleTV.

The movie is Batman (the first Micheal Keaton Batman movie) and I'm currently using Handbrake because it's worked great on just about every other movie I've tried to convert. I have also tried several other converters and had the same problem with Batman.

My problem is that the video and audio are out of sync, but the weird thing is it's just the AAC track, the AC3 track is fine. On both the large and esmall videos the AAC was out of sync, while on the big video the AC3 audio track was fine.