Random Video Noise in Compression

I have a 90 minute timeline that I am exporting to Compressor - using DVD Best Quality 90 Minutes 16X9 - each time I do it I get random video noise - pixalated blue boxes - bands across the bottom of the screen etc. Each time I compress the noise is in a different place. With Compressor 1 I did not have this problem. I have a number of Chapter Markers that I am exporting and quality is a concern so I need the Dolby 2.0 compression on the audio - so using the Quick Time Conversion is less desirable - I have followed the directions for getting rid of Compressor 1 presets but they don't seem to go away - also tried to reinstall compressor but on a custom install it is grayed out. Any suggestions? I am desperate!

Geoffrey,
First a speed issue (Compressor 2.0.0, solved in 2.0.2) then there are gamma issues (still broken), now I too am having video noise in the form of strange bands / chunks and lines in the video. I've checked my master, the digitized source in FCP and it definitely is in the output from Compressor. My source material is uncompressed 10-bit 4:2:2 footage from both Beta SP and Umatic. I export to a Quicktime reference video (because a direct export fails to incorporate proper gamma settings, the image being too dark) and then import into Compressor.
My System (all software, drivers, and firmware up-to-date):
Quicktime 7.0.2
Compressor 2.0.1
FCP 5.0.2
OS X 10.4.2
Aja IO Driver 2.0 / Firmware 23 (28)
Xserve RAID Driver 1.0
G5 Dual 2Ghz w/ 4 GB RAM
I'm happy to provide Apple with any footage for troubleshooting purposes.
BTW, I recommend rolling back to (or staying with) system 10.3.9 with FCP 4.5 and Compressor 1.0 for anyone considering the jump who need MPEG2 compression out of Compressor. That system runs fine.

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