If you add a Shapeless Arcane recipe with Modtweaker things get slightly weird.

Issue 1:
Somehow one item acts as a .reuse and isn't being used when the crafting is done. The items used also go directly into the inventory, sort of if you use a bucket in a recipe and it goes directly down into your inventory.

Issue 2:
The recipe does not use the ingredients (except on the first click). You can keep on clicking on the item output even if the ingredients are marked with a null in the grid. Example

Issue 3:
Shift-left-clicking the output item to craft all the items in the grid in one click it crashes to Desktop. Jared you have the log :P

Log for reference, once again, it can't be us...
http://paste.ee/p/GeIXK