Even if the room type is set to special item and the item is included and Link visits the Item Cellar or Passageway for the first time, the item doesn't appear at all.
Item doesn't appear in Item Cellars or Passageways [448]
That's those flags in the dmap screwing with everything.
Crap, this one's my fault, caused by the shop/info room fix. Fixed in the next build.
Bug confirmed fixed in 461. Item is available until Link grabs it. Dead bug. 😉