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Are you sure you are using the same encoding profile that you were a few months ago before the problem started? Are all of your codecs the same? Is the color space different ? I would bet on color space conversion issues myself, but that is a wild ass guess.
Also, unless you are using a lossless codec you will experience significant generational quality loss. A lossless codec would be something like lagarith or cineform.... actually cineform's 8 bit is only visually lossless and then only through a few generations and without significant color converting back and forth.
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