Can't get a clean m2v no matter what - please help.

Folks, I've been working on a project about an hour long that will not yield a good DVD using Apple products or Toast. I keep getting subtle digital artifacts in different spots. Sometimes when I recpature footage and think I've fixed it, then recompress to make my dvd files, the artficacting shows up somewhere else. When I make a small Quicktime from my timeline that had the problem after compressing, the artifacts don't show up. The Quicktime (for the full show) is otherwise clean, but when I compress it using Compressor (90 minute best DVD) or let DVDSP4 encode it, i get problems either way. This happens both using Leopard and Tiger (as I tried these compression tests on two machines). I am at my wits end. Does anyone have any advice here. This is a mission critical situation and have never had these issues before.
Specs:
- DV NTSC Quicktime made from FCP 6 (FCS2)
- Leopard/ Tiger (both yielded same results)
- inconsistent artifacting
- Used Apple DVD compressor settings (not custom)
- Used DVDSP 4 for encoding
- Final Cut Studio 2
- Tried it on G5 dual 2.5 and MacBook Pro

This was true with V2 of Compressor, but v3 is actually far superior to BitVice or even Episode Pro, especially when it comes to down-converting from HD to SD-widescreen.
We just spent a few weeks thoroughly investigating and testing various software-based encoders: Compressor 3 (C3), Episode Pro, Sorenson Squeeze and BitVice.
Both Squeeze and BitVice have not had any major updates in over a year and are behind the curve when it comes to output options and overall quality of encoding. BitVice does not handle down-converting HD-to-SD well at all in fact, even at it's best settings caused visible compression artifacts not seen with other encoders. Episode Pro is extremely fast however their MPEG2 files are not compliant with DVDSP4 creating stutter and strobing playback. This is a known issue that Telestream has been working on but so far has not been given much assistance from Apple in fixing the issue.
The major complaint about C3 has always been it's speed - or lack thereof. However on our Leopard test-bed we found - as others have - that Leopards' thoroughly revised memory handling and complete redesign of hardware/software rendering engines have significantly increased C3's speed and accuracy.
A year ago BitVice was a serious and often preferred contender for then Compressor 2 however for the Mac there is no better encoding engine at any price than C3.
If you're having issues getting acceptable results from C3 I highly suggest the "Compressor 3 Quick Reference Guide", by Brain Gary. It's a quick read and I'd advise paying attention to small details since it's always the "devil in the details" about any encoding engine that seems to only show it's ugly head after testing.

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