I’ve never used Syntheyes before, so this might sound ridiculous. Can you export the raw tracking data into AE like you would from Mocha? Or how about export just the Synth camera, and use it with your footage in an AE comp to perform the stabalizing? Then you can add the motion tile or CCrepeTile and all would work fine.
Believe it or not, you can use the titler to make the track matte. Use the pen tool to draw a white filled bezier. Then use it instead of the Photoshop file as Mike described above. Add a blur to it if you want to soften the divide.
Start learning about the CS3 graph editor. Unfortunately, the implementation of this tool is very crude and still in it’s infancy. But it does allow you to recognize and fix issues such as this immediately.
Does this happen if you start a new project? If not, maybe your project file is corrupt. Try importing this project into a new one and see if it works. Or maybe open an auto-save of the project from before the audio issue began.
I don’t think ripping a DVD is illegal if you are using it for the purpose Mike is intending. I have used a program called AOA DVD ripper in the past to extract individual scenes from a movie with good success, and I’m sure a google search will provide links to more modern software apps. The only issue you may run into is if the DVD has copyright protection and can’t be ripped.