Thanks for playing PikaMew! So. . . yeah, the auto equip thing I should have done better. Basically the items auto-equip when you load a new game. I was assuming players would equip the items as they opened the chests, and the auto-equip on loading was meant to ensure that meta-equipment would magically be equipped, even if you load an old save file.
But I neglected to make the items auto-equip as soon as you open the chests, which can cause confusion. This is one of the many ways I tortured myself with the Meta Stasis concept, and the fix didn't make it in before Jam submission.