In case anyone is uncertain how to replicate the problem:
(1) In the options menu, turn off everything under "Automated Hotbar Behavior."
(2) Learn the Polymorph skill "Medusa Head" (other skills have the same problem, but using this one as an example)
(3) Activate Medusa Head. When activated, the skill "Petrifying Visage" appears in the skillbook.
(4) Open the skillbook and drag "Petrifying Visage" to the hotbar, so that you can use the skill.
(5) Save the game.
(6) Re-load the game you just saved.
(7) "Petrifying Visage" has now been deleted from the hotbar. It has to be manually placed back on the hotbar again in order to use it. Every. Single. Time.
