The quick answer is I don't think you have a problem CCD. What you are seeing is the sensitivity of the CCD to a blue sky in the different channels. As an example, for my monochrome CCD, when shooting dusk sky flats, I have to stack my series so that I shoot with my red filter first, then green, then blue because red is the least sensitive, then green and blue is the most sensitive. I need that to get comparable ADU counts with comparable iteration times. That is exactly what you are seeing in your color flat but compressed because all the channels are being shot at one time.
Sadly, since I have never worked with flats using a color CCD, I can't tell you how to deal with that issue.
Hope that helps,
Jim