I've built a system to manufacture coolant cells for my nuclear reactor using automatic crafting table mkII's. The one that makes the water cells works fine, but the one that makes the empty cells doesn't. Through google, I found out that the tin ingots in the crafting table all need to be in their own space and the recipe won't work if they're stacked. The problem is, they're put into the table by buildcraft pipes and the tin just stacks on top of each other in the table. How do I prevent this from happening?
It turns out that BC pipes aren't properly compatible with automatic crafting table MKIIs, so RedPower tubes must be used. BC pipes will still work if the recipe does not contain more than 1 of the same item.