This may or may not be a bug, but currently the clickable areas to set Link's graphics are always set to the 16x16 size boxes. The way I seem to remember it, it was always the lower and lower center 16x16 boxes that you'd click to set his graphics for 16x32 and 32x32 respectively
I don't mean the tiles in the tile pages, I mean in the Quest > Graphics > Sprites > Link dialogue box. On the tile pages, the aforementioned lower/lower center selection works fine as always