Yeah, so I'm going to go test out some stuff I put into my quest and notice that I have a big key, map, and compass, as well as all the triforce pieces in town. WTF? So I went and checked my Init Data and sure enough, every level in the Init Data has all three checked as well as 1/2 Magic and all the triforce pieces. I unchecked them, saved the quest, and they went away until I opened my init data again and they all rechecked themselves. I tried to duplicate it using a new quest, and it happened right away.
Open a new quest, check like, level 1 or 2 for maps and compasses, press okay, then open up init data again and everything will be checked by default.