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I've used the "create reference frame" too, since R3 came out. Like you said, the difference sometimes can be subtle but I can understand why it's there and why it would work well..
As bird said, slight adjustment in the wavelets screen, then go back to align, and it's looking for frames that look more like the final result you want. It should rank the truly best so you can eliminate the bad ones with the stackgraph slider.
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