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John,
I use Nebulosity and in that you can do a registration without stacking and keep the files aligned but separate I know Pix Insite can do this but I'm not a fan of slow Java based software for number crunching.
That way you have a set of images all aligned and you can do other things like statistical weighted stacks to remove wild card CCD errors and also have the files aligned very well for LRGB in photoshop.
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