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Hi DJDD, I find Deepskystacker actually does much better with the RAW files than anything else..well with the canon anyway.
After you let deepskystacker do its stuff and you are previewing the image, you have some settings for levels, luminance and saturation , you can bump up the saturation to 15-20%. That should give you a close to natural color saturation. remember to tick apply changes to image when you are at the save dialog box.
Hope that helps..
cheers
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