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You have to be quite strict with the images you reject from the stack.  I had about 12 images I rejected as I didn't think they were up to the quality of the others.  I also edit all mine in sync within LrC before I export to Ps to ensure that the images are as close to each other as possible.  I also centre the cropped images as best I can in LrC before I export so that the aligning process can work.  I've found that if the moon crops are not positioned almost identically, the stacking can fail or produce poor results.  Not sure if that helps, but it is worth trying again.