I am home now, so I have access to the game. I have both Map Pins and Lore Books. I see all books on my Compass.
If I set the option to show unknown Eidectic Memory books on the Compass, they show up on the compass, same with Show Lorebooks on Compass.
Map Pins is set to show unknown books.
So either something is not set right, or you have an another addon conflicting or your Lib Files are not updated for all mods.