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As Robert has just said try the RGB realign in Registax and see how that goes. If not (and I still work by "hit and miss" and "trial and error") try saving each individual bmp and then opening them in registax and processing it theres.
Actually before I go on, how/what are you capturing (capture combine or capture and save each bmp)? What are you using to process? And do you have K3CCDTools Version 1 (Its free you just need to download a new key every couple of months. Unless you buy it of course, then buy Version 2 and you get Version 1 thrown in)
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