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Mick - whenever I'm aligning frames that I've pulled into Photoshop and that reside on separate layers, I usually use guides to help me. While showing just the base layer, I pull both horizontal and vertical guides in to intersect a bright star at the top left of the image and then repeat for a star at bottom right. In your layers palette, deselect the base layer view and select the next layer. With the Move tool selected, tweak its position until the same two stars are intersected by the guides. If you flick back and forth between the layers being viewed they should all line up with the chosen intersected stars. Maybe view it at 100% to be more accurate.
When you have all the layers aligned manually this way (as long as you haven't suffered rotation - which is a bit more complex to fix) you can convert the layers to a Smart Object (if you have CS3 or newer) by right-clicking in the layers palette and then choose the appropriate stack mode from the Layers/Smart Objects/Stack Mode menu. I usually use "mean" stacking here.
Does this help or am I missing your intention?
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