Gil, do you know why shortcut slots are not saving for weapons and items? 
For example, for a weapon, I open up the inventory menu, drag a sword to the shortcut slot 1, and the sword is now in slot 1.  If I change scene, the sword will still be in there, but if I save the game and come back, the shortcut slot 1 is now empty.
Same for the item, but it behaves differently.  Let's said in Inventory > Items, list number 0 is HP Potion and number 1 is Poison.
In gameplay mode, if I open up the inventory, drag the HP Potion into slot 1 and save the game, upon loading it, the hp potion will still be there.  But if I drag the the poison into slot 1, save it, and load the game, the slot will be empty, except that if you hover your mouse on the slot, the word 'HP Potion" can be seen in it.  It looks like after loading the game, the slot removes the item in it and just replaces it with the item from the number 0 item in the Inventory > Items section, whatever that item may be.