When you right click on a piece of equipment with an empty charm slot, what is listed in the menu that comes up? Is there any difference if the gear is equipped as opposed to just being in your inventory (other than 'equip' changing to 'unequip')?
You should be able to add charms to equipment as soon as you have a charm and something with a charm slot. AFAIK nobody has mentioned anything weird with not being able to add charms if the game was paused, or not paused, etc.
If there was just a glitch with the game not recognizing that you have charms, from outside the battle tower try right clicking on all the charms you have and sending them to the battle tower, then return to the battle tower, head to the chest in the master's chamber, remove a couple charms, switch to the inventory window and right click a piece of equipment with a charm slot. Maybe that will get the charm entry showing in the equipment right click menu.
