Process to reproduce:

1. Set up one machine that can craft two items. I used a Metal Former from IC2 Experimental, set up with the ability to make Iron and Tin Plates
   2-4 Must be done quickly or use a crafting method that takes time like the Metal Former/Auto Crafting Bench from Build Craft
2. Request 1 of Item 1
3. Request 1 of item 2
4. Request 1 of Item 1
   

Result:
Item 1 is created and left in the output of the machine
Item 2 ingredients are pulled to the machine ready to be crafted.
Because the output has the result of crafting Item 1 in it the process stops

Crafting logic has been fixed slightly. See if it works correctly now.

If the crafting pipe is configured right, that piece should also be extracted.. (And, I know, very delayed response. Forgot about this..)