If you do the DoT Skip with a rather small inventory, it is possible that at some times you will not be able to equip certain items like the hookshot or ocarina. This is because there aren't any other items on the same X or Y axis of that item.
There is a way to get around this. The reason this occurs is because you start on the Map Screen when a file is first loaded, and have to scroll over to the Item Screen. Therefore, if you pause in any area in the game, unpause, and go through a loading zone to a new area, when you pause again the screen will start on the top of the Item Screen, allowing you to progress downwards to the item you want.
In a segment if you did not need to pause, you would have to waste time pausing and unpausing, which wastes a second. In order to avoid this, simply kill yourself, say No save and No continue, and then load the file. This time, the first time you pause it will be on the Item Screen instead of the Map Screen.