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Hi Mark, I have had the same problems with separating colours after stacking and combining. You may find it is a combination of camera tilt in the focuser and also a registration problem due to field rotation. I found the requirement for a very good polar alignment and a very good reistration alignment program made a great difference. CCD Stack give the greatest flexibility in registration and alignment I have seen in quite a few software packages.
The incorporation of these two items returned me quite good results but as always, at a cost.
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