So as of last week this problem "fixed itself". I turned on my Kindle and wifi one day, and all the new books that I had queued for download over the last few months (that I had not caved on and manually downloaded), and titles that I had chosen to update via "My Content and Devices," started downloading to my Kindle. The X-Ray works for them as well.
So as I suspected, it was likely an Amazon server issue, and they've fixed it.
-HM
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