I think that we are dealing with different situations as I was making a quicktime to project and your workflow is through iDVD.
Kind of hard to remember back a year ago, but I believe my issue was actually a discrepancy between the way that NTSC displays on a computer monitor vs. a NTSC monitor.
That being said, I have had to continue to tweak things whenever I deal with any NTSC encoding. I always seem to have surprises with the aspect ratio. Usually an issue of getting the right settings for the pixel aspect ratio and the overall geometry/aspect ratio of the video.
I actually rarely make DVDs and if I do it is with DVD studio. The issue could be in iDVD and you might want to check the forum for any issues there.
One other thing, make sure that you have your NTSC monitor on the right setting. Some monitors you have to manually switch from 4×3 to 16×9
So, a few things that I would recommend experimenting with.
1. Try a different exporting method from FCP. My normal workflow is to export a reference movie (I think that I go over the details of this in my original post) which keeps FCP 6 free for doing more editing. Also, sometimes exporting using Quicktime conversion seems to eliminate NTSC aspect ratio problems. But, Quicktime conversion also locks up FCP and is not the most efficient way to use your computers resources.
2. Try editing the inspector properties for your mpeg. Under the Encoder tab, and the Video Format tab within that you have options for changing the aspect ratio and field dominance that you will want to check.
3. Once you have all of your settings in inspector you can try to check the results in the preview window of compressor (select the full clip, not just the setting, in the jobs window). Under the scaling pull-down menu there is an option to turn correction for pixel aspect ratio on and off. This might help you get a sense of what your output will be like. Also, try switching between the two buttons in the upper right corner of the Preview window. This will switch between the SOURCE and SETTING aspect ratio.
Okay, those are my suggestions for now. Good luck. Keep experimenting (perhaps with some 20 second clips).
-Matt