I bet the problem is what Harry pointed to... I had a plugboard step for azw3 files, but some of the files is sent to my Kindle were mobi. Took me awhile to realize that I was sending mobi files. inadvertently--in my case calibre's default was set to transfer mobis first. After I figured that out and set Calibre to choose azw3 as the transfer format first-- everything worked as expected.
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