A-ha, mystery solved! They're the Gentian Shoes from the Pixie Post Office - the long Gentian Skirt usually covers them up so I didn't see them in-game very often.
You were on the right track, Tiramisu - some of the older DS outfits got an improved design and were released in the Pixie Post Office (that's why some items are called "Original Top/Skirt/etc" to avoid confusion). The Gentian dress was one of the outfits with a new version so that pointed me in the right direction.