Okay, so I solved the problem last time. For whatever reason, if you get the Fire Rod before the normal magic wand, the Fire Rod is put into that slot as well. But it resolved itself once I picked up a proper magic wand.
Anyways, there's this really confusing sidequest. At one secret shop on the island, you can buy compasses that point you to hidden rooms in the shrines, which contain statues. Since I'm playing Grand Tour mode, I had 48 shrines to do, and I got all of the statues in them.
However, there are hints by each statue such as "Buying antiques at Brown Waterfall Rock!" and "The truth is only available to those who can dive down below". I can't find this place to sell the statues, and although I collected all items from shrines (including the four Elder Shrines) and overworld, none of them were the flippers. I suspect I may have to trade the statues for flippers at this antique shop, but like I said I can't find it. The compass shop WAS in a waterfall (accessed by ocarina to make platforms to it), but there's nothing to do there besides buy more compasses and potions.
Anyone know what I am missing here? Thanks