Items in the imbuement chamber and on arcane pedestals are invisible, and also don't get listed in any hud element when targeting the block as near as I can tell which makes it a bit tricky to debug sometimes. Interestingly the central item in the enchanting apparatus seems to work ~90% of the time, and floaty items for the scribe's table work just fine.

99% I would bet this is Rubidium, Flywheel, or Starlight.

Likely Starlight, Rubidium and Flywheel are commonly run and users have not had issues with those in particular. Likely something they do to Item Entities.