So, to restate the issue in the same thing that has happened to me:
Ingredients are piped into the side of the Automatic Crafting Table MK2 with a stone pipe.
The Output is piped out from the top, using a Wooden Transport Pipe, powered by a Redstone Engine.
Ingredients go in, ingredients begin to stack. My example - Bronze dust (3 Copper Dust, 1 Tin Dust)
Ingredients reach 3 Copper, 1 Tin, and nothing happens. No Bronze dust is extracted.
What I have found is:
If you quit out to the Main Menu and then reload the world, the Bronze dust starts to get extracted.
And, importantly:
If you leave it for the ingredients to fill a stack of 64 for each, then it starts to craft automatically.