1 is the binning for color imaging. 2, or 4 are what I use for focusing and are B&W, because 1 gives a lot of distracting colorizing.
I always use my Bahtinov Mask for focusing, and have an electronic focuser I absolutely love for fine focusing remotely.
As for your color issues, I really can't advise, don't know.
But I wouldn't sit around, find out if it's your telescope, or the camera. (I'm betting on telescope issues)
Are you using a high quality imaging telescope? Lesser telescopes may be the culprit.
I didn't want to deal with any of the typical needs of various telescopes, so I'm Galilean, I chose a Refractor as my weapon of choice. And because I hunt Nebula, and I consider my telescope as a camera lens, I got a Triple Apochromatic telescope.
Been quite happy with it. And it was about my budget limit at the time.
Forrest Tanaka put it best, Astroimaging is one of the hardest types of photography there is. But it is also one of the most rewarding. I hope I can share a link here,
http://youtu.be/9d0292TBMHoIt starts right off with telescopes and astrophotography.
So if your telescope is up to it, than possibly your camera has an issue. But I trust Atik quality. So that's why I wonder about the equipment around the camera.
Reference:
http://www.baader-planetarium.de/atik-kameras/download/Atik-Infinity-Quickstart-Guide.pdfAnd I'm finding that tiny adjustments to the Histogram are better for me. Note the settings displayed in the Quick Start guide.