Yeah, I'd heard about that one, but I'm not at the same point in the game.

I feel like a complete idiot now, though. I figured out what the problem was. Apparently I've been playing the entire game, since getting the Master Sword, without actually equipping it. This leads to both a sense of stupidity after trying to figure out what the problem was for an hour, as well as a slight sense of pride for playing most of the game with an inferior weapon.