Compressor quality changes with clip length

Hello,
Im on a max OSX 10.6.5, compressor 3.5.3, FCP 7.0.3.
I am taking footage off the SONY XDCAM, running it through the XDCAM Transfer software and having it wrapped in quicktime so i can edit in FCP. The project was filmed in HD 1280x720, XDCAM HD422, 720p60(50 mb/s).
The destination is SD DVD.
Problem- Since going from HD to SD can be a bit tricky, I made a half dozen sample compression clips. I found that the compressor DVD 90min Best quality preset with a slight bitrate change to look the best. When I compress the 3 minute clip, it looks really great. But when I compress the entire sequence (only 83 minutes.. well within the 90 minute preset) it looks like garbage. The difference is night and day. What is the issue? suggestions?
Thanks,
Brian

Sorry for the slow reply, I hit the road for a while shortly after posting...but I'm back.
Also, I'm embarrassed to say that the problem turned out to be the nut holding the tool (in other words, user error). It doesn't matter how carefully one changes the clip length if you somehow forget that clicking on the clip then selecting "pasteover at playhead" does not paste the selected clip but pastes whatever is in memory. As I'm sure you can guess, the clip copied earlier was 3:12 in length.
Sheesh.
Sorry for the false alarm, and thanks to both of you for the help.

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