So, you have 3 refined iron along the top, 3 bronze along the middle and 3 tin on the bottom?
Your stirling engine is also powered by a redstone signal with fuel (any burnable item)?
If you only put one of each item into the crafting slot, you click on the MMI above the progress bar to get it to use the last set? (If you have multiple items per slot then it will auto craft them).
I'm just covering everything here as I have just tested it and it worked fine. If you are still having problems, post a screenshot as pictures can be clearer than words.