Spells disappearing on equipment change

I'm having a problem where some of my equipped spells are disappearing from my bars when swapping in new gear. Also, they're no longer listed with my other spells when I click my bar to assign them to a key.

It seems to only happen when I change my boot equipment (I've had to use the same boots for the last 10 levels or so because my main attack disappears when I equip an upgrade).

And no, it's not that the spell is being unequipped or anything like that; it's removing spells that I have on a completely different item slots

It seems to (so far) only affect my freezing pulse and ice spear spells.

Any thoughts?