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G'Day Trevor,
Not that I've done any LRGB imaging myself, but I've played with Layers and masking a bit.
It may just be that PS only allows you to move the layer by a whole pixel at a time.
Try resizing your image up by say 4x prior to aligning the layers. Once aligned resize the image back to original size. That will give you at least 1/4 pixel alignment accuracy.
Al.
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