Problem Solved.
I finally noticed that both out of order books had the same problem. The metadata Author (not the Author Sort) were different from all the other books. In the Potter books the problem book Author began with "by J. K." instead of just "J. K." and the Pendergast series had a book with a slightly different Author name.
What this tells me is that the Kindle Author sort is not by the Author Sort metadata. It uses the Author metadata. That seems like a poor decision to me.
I've updated the Pendergast series, rebooted and confirmed that the sort is now correct.
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