Like the title says, when you make an item with scripting, the area that Link could grab the Item is very small. The Collision box instead of covering the whole item, it only covers the left wall of the Item. In the test quest, there will be 4 blue keese. These Keese drop items normally, no scripting involved, they should drop 100 rupees. Notice how if you touch even close to the item, you'll pick it up, and that the boomerang can also easily pick it up. Now in the 2nd room, there will be 2 red Keese. They drop Heart Containers that were spawned by scripting. Notice how when approaching from the right, you have to go all the way to the left to pick it up, and if you throw a boomerang vertically it will not grab the item unless it touched the left side. And if you boomerang the Heat Comnatiner, and run to the right while it comes back to you, it will stop and you wan't grab it. Just to have even more evidence, feel free to enter Cheat Level 4 (The Cheat is the number : 4) And if you enable the Cheat that allows you to see Hit Boxes, you'll notice that the collision, what should be a box, is just a line for the script spawned items. It's as if there is no horizontal setting for the box.
Test Quest - www.garyshood.com/steven/ZC2.11/Item_Collision_Bug_Test.qst