I have had a similar problem. My problem was using the cheat that gives me the goron tunic without getting it from the goron, and then the game not opening the door to the room to go to the Fire Temple. In the game's code, recieving the tunic from the goron is the trigger to open the door, but if you already have it, then the game thinks the door is already open. I don't think there is a workaround. The only way to fix your problem is to play the game without this code until you get past the point.