Update and thank you all that helped or continue to help solving these issues:
Issues:
1) "You cannot combine these items in this container type!" warning, most certainly from me having an incorrect setting somewhere in the item editor for these items/box or in the recipes listings.
Custom container flagging solved.
2) Having multiple items on your cursor is always a bug with the server, so returning the output item plus the box could trigger this bug as well.
Not yet solved, and a larger issue than simply this functionality. Anytime multiple items stack on the cursor, only the top item is retrievable unless the character camps and returns, then the next item is on the cursor. 
3) How can I create multiple acceptable pairs of items in the recipe using the same container?
Multiple recipes correctly inserted into database and this now works, solved.
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