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What "command" are you using Pete? I just had a real quick look at the Help file online and it appears the "Stack" command is what you need.
CCDStack is my choice, but I did see Maxim simply gobble up the required files and spit out the result, no pointing it to this frame or that, simply spat out the result, amazing. (and that included a binned RGB as well as a normal L).
Gary
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