Why is Audio out of sync after encoding?

I have encoded a 60 minute film using separate video and audio files -- quicktime for picture, AIFF for audio. In the DVD Studio Pro project, they are perfectly in sync. But in the encoded DVD they are playing out of sync by over 1 second.
I've encoded the same movie with different versions of the soundtrack several times before with no problems.
Anyone have any ideas of what has happened and how to fix it?
The Quicktime and the AIFF were on different drives when I was building the project. Could this have had any effect?
Using DVD studio pro v4.0.2
Powerbook G4   Mac OS X (10.3.9)  

Nope, I am a strong believer if it ain't broke do not fix it, and personally I loved 10.3.9 - in fact I say away from updates unless absolutely needed and then I bring them onto different machines. Unless something changed in your system, I would try standrad troubleshooting (repair permissions and delete prefs) and A.Pack the audio
Not to say I do not have machines running Tiger, but Tiger (particularly some of the newer versions) I find to be a PITA - around 10.4.6 or so there are weird security things happening which messes up installing software. In fact I just zeroed out my tiBook, and did not add some software that I forgot about until after 10.4.8 was on and it does not install. I would have to zero things out again. Install the software over 10.4.1 and then try again.
Unless you want the Universal Suite (which is good for most things except DVD SP which has issues) nope, no Tiger none of the new stuff, unless you have a few machines to play with

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