It sounds like you might have the pet hotbar turned on. It's an extra hotbar that gets added whenever you change to a class with pet actions and for whatever reason seems to overwrite the normal hotbar cycling and changes it so that simply tapping R1 toggles the pet bar on or off.

The good news is that there is an option to disable it in the config and all you have to do after that is place your pet actions on your hotbars like normal actions.