Update:
It appears that for JAWS OF HAKON and TRESPASSER the Keep was unlocking choices, but not assigning them to the tapestry, so I could go in and select the choices I had made.
The Keep did not unlock or record choices made in DESCENT.
It also did not unlock or record any choices in Operations when playing the base game.
So the Descent and Operations issues were a bug, and the Jaws of Hakon and Trespasser issues were not necessarily a bug (since they unlocked), but just didn't display as "chosen" until I did it manually.
I turned on the Show Spoilers in the Keep and selected the choices that I made for Operations and Descent, so I guess I'm good now.
