Okay, this one, I am not understanding that much, so I will tell you want I exactly did.
I have no items whatsoever. So the cursor is automatically on the boomerang spot. Then, I grab an item like the sword, the cursor is still on boomerang spot. So I move the cursor to the sword to pick it, however, if you try to put it back to the boomerang spot, ZC crashes.
Because it still trys to move to an item that isn't there and it freezes when it does that. I did it all 3 times I tested it too.
I can't seem to replicate this. I set the appropriate quest rule and then grabbed the Wand. I got the behavoir you described of the cursor staying on the Boomerang slot, but Zelda Classic didn't seem to crash no matter what I did. I tried assigning the blank slot to A and B(both kept the spot, well, blank, and there was no crash when I tried to use the blank item), and as soon as I moved the cursor to the Wand, it was stuck over the Wand with no way to move back to the empty Boomerang slot. I could move the Wand between A and B freely, and there were no crashes associated with using it or attempting to use the blank spot. Is it possible that there's something wrong with your custom subscreen that's causing this, and can you replicate it with the default classic subscreen?
Well I don't think it should be crashing in the first place... But let me see. I do have the rule of (A and B button to be used). But I tested it again, and it is when I pick up the sword (I have nothing else in my inventory), and then I set the sword to A. Then I move back to the boomerang spot and it crashed.
But I didn't do anything really to the custom subscreen, I just changed Farye(sp) Wind into the Sword, and that is all I done to that subscreen thus far.
That's the odd thing. I tried what you did and used the Revision 2 subscreen instead of the Original one and even used Farore's Wind, but after moving the cursor to Farore's Wind, it simply wouldn't let me move the cursor on the subscreen again. It was permanently stuck on Farore's Wind, and I couldn't move it back to the Boomerang slot. I tried it after swapping Farore's Wind with the Wooden Sword in both the item I grab and on the subscreen, but the result was the same. All I've done is on 278 with nothing in my starting inventory (the same as you) so I'm not really sure what the difference is that's giving you a crash and me ordinary behavoir. This does sound like a rather serious bug, but it must happen under some pretty specific circumstances or something.
Send a copy of the quest that's doing this.
It was fixed, just to let you know. sorry, I didn't get to you sooner. >_<