This is a feature that X implemented, where the ever-so-helpful manufactories think they should be off unless:
* There is a negative drain of the type of resource the manufactory produces
* The banks are empty on the type of resource the manufactory produces
* There is a positive income on the other type of resource (that the manufactory does not produce)
* There are remaining resources in the banks for the other type of resource (that the manufactory does not produce)
Can you tell i don't like this feature? There's a control node that deactivates this behavior though. I honestly think it should be changed to:
* the production of the other type of resource (that the manufactory does not produce) is higher than the production of the type of resource the manufactory produces
* There are remaining resources in the banks for the other type of resource (that the manufactory does not produce)
so it runs to level your income. Plus, if not already, there should be a tooltip that states they control themselves unless you turn that off.