You're showing a *Collection* in that screenshot. I'd wager that the books inside are indeed tagged EBOK, except the ones sent by Amazon.
How the Homescreen shows collection has somehow always been confusing to some, so it's not unheard of
.
(Basically, Collections, Clippings, Kindlets (apps) & Booklets (super-apps) are special types of items, and may or may not appear as you would expect depending on which filter you're using on the Homescreen).
To recap how Calibre's PDOC feature work: in the mobi output settings, it asks you for the name of a tag. Any books containing that tag will be tagged as PDOC instead of EBOK during the "Send To Device" process.
As usual, when updating books (and not uploading new ones), keep in mind that the Kindle DB is tricky, I recommend deleting the books from the Kindle's UI first, to avoid weirdness.