Blue lines in MPEG-2 compression

The source is from a ProRes mov file, the length is about an hour. But this ONE SECTION of less than 1 minute is producing some flashing blue lines on the top of the screen.
It is NOT present on the source timeline nor the source quicktime export.
I've tried EVERY setting of upper first/lower first. But the only way the blue lines go away is if I compress as PROGRESSIVE.
But I can't compress it as progressive, because it looks stroby and looks bad on a TV. (Looks fine on a computer)
(I've also tried compressing in Adobe Media Encoder, and Cleaner XL) (same results)
What can I do to fix this? Help!!
Here is a link to a screenshot.
http://i28.photobucket.com/albums/c212/starterkit/blue.jpg
edit:
The final output for this file is DVD Studio Pro.
Message was edited by: Ryan Aquino

It sounds like you are Sending to Compressor directly from the FCP timeline. You can try exporting out a standalone QT movie and then encoding that with Compressor. Or you could render/export a standalone movie of that section of the timeline, reimport, and then try Sending To Compressor from that sequence.
BG

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