Empty pixel color

I am a professional photographer who normally shoots a Canon 1Ds Mk III and a 5d. I long ago noticed that when I pulled my images into Lightroom - particular those shot at high ISO in low light - there would be a slight shift in color, usually to the detriment of the image, after I selected it.
Very recently, I suffered a bad accident that put me in the hospital for two surgeries and now I am convalescing with an artificial shoulder. That same accident knocked my 5D out of commission. While I have done no real work since, I kept shooting for journal purposes, but with only my left hand, it was extremely difficult to use the M III and so for my birthday, my kids gave me a Canon Powershot G9.
While the G9 is great fun and has decent IQ at the low ISO, it is extremely noisy at high ISO. When I pull low light, high ISO G9 images (I shoot RAW, btw)) into Lightroom, as noisy and grainy as they are, the color balance can appear to be close to perfect and the effect nice - UNTIL I select an image. Then it suddenly takes on terrible burgandy cast.
So I finally figured what caused the slight color shift, even with the 1Ds. Lightroom is taking all those empty spots and is filling them with colored pixels that together create the burgandy cast. This makes color balance almost impossible, as the invented color in the filled in area has nothing to do with the original colors of the image.
Is there anyway to control this? It seems to me that if I could set Lightroom to fill in those empty areas with 18 percent gray, instead of the arbitrary color, this color shift could be avoided.
Any suggestions?

The color shift you are seeing is actually caused by Lightroom first showing the jpeg preview embedded in the RAW after which it shows its own interpretation of the RAW data. Read this FAQ for example.
http://www.adobeforums.com/webx/.3bc3d55a
Lightroom simply has a different interpretation of the RAW data than your camera. Apparently Lightroom 2 might have a solution to this issue. You can also calibrate Lioghtroom/ACR to your camera at the high ISOs using a colorchecker chart to improve its color rendering.

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