Artifacts in Encore Build

We built an ENCORE file from a QT MASTER (895 gigs) which was originally exported from a FCP MASTER.
In the ENCORE "BUILD" there are white specks and black specks/artifacts, particularly where there is a higher level of bright light.  i.e. when a headlight shines on someone's face. 
These issues appear in the exact same spots every time.  We burned a Blu-ray disc and they appear in the exact same spots as well.  So I don;t think the issue is related to the cables or TV (because it is in the ENCORE BUILD as well)
NOTE: 4 weeks ago, we had previously performed the exact same process, using ENCORE, with the same Blu-Ray burner and there were NO issues whatsoever.  Since then we have added about 2 minutes of footage (including a 10 second green screened sequence) to the master FCP MASTER, which looks great (no artifacts) then exported to a QT Master, which also looks great (no artifacts), then built it on ENCORE.  Now we have this issue with the specks/artifacts.  
Anyone have any answers and/or solutions?
Thanks,
Jay

Thank you, Jim,
MAC OS X 10.6.8  - 12 core, 8TB
Processor: 2 x 2.66 GHz 6--core Intel Xeon
Memory: 24 GB  1333 MHz DDR3
ENCORE:  Adobe Encore CSS Version 5.0.0  
Yes, 895 gigs.  We made an independent movie about homelessness.  A full feature.  Running time with credits is 1 hour and 52 minutes.  
The final master is at 895 gigs.   About 5 weeks ago, when the editor built for blue-ray on encore before and burned blu-ray discs on the same burner and this same computer, there wer no issues at all.   Since then there were a few more scenes added in FCP, then exported to a QT Master (adding about 30 more gigs).  
The editor wen through the exact same process and this issue with the artifacts exists.  Also, the single ine credits are over white and the black text is sort of greenish.  Then more single card credits appear with white text over black.  They are fine. Then at the end of single card credits, just as the crawl comes up, the first line in the crawl is very faded, then corrects itself.
All of the issues in the movie are in the exact same place. we have tried them on different tvs and the same issues are in the exact same places.
He tried it again and it still exists.  Although he will be back on Monday, he is at a loss and will try to research this as well.
I assist the producer director who has been editing with the editor.  If you like, he can converse with you directly although he is not any more tech savvy than me.  And I'm sort of a newbie.
Thanks again,
Jay

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    Hi,
    Sorry if this is a newbie question, but we just can't figure this one out.
    We built an ENCORE file from a QT MASTER (895 gigs) which was originally exported from a FCP MASTER.
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    Thank you, Mylenium,
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    But can you tell us what difference it makes what the FCP export settings were since we exported to a Quick TIme Master?  It was the QT Master that ENCORE worked from.

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