Andrea, I'm sorry for the late reply. But in the meanwhile, I did a lot of testing. The result is interesting:
When I open manufacturing central, and I click one stock, click 'set' and click 'save', it works fine. The stock of the end product changes in the expected value.
But when I change more then one stocks (so the number in several rules is red) and I click save, then the new values are saved, but for only one end product, the stock is calculated into the expected value. For the other end products, nothing happened. When I just click the (allready changed) new stock per rule in manufacturing central and click 'set' and 'save', everything works fine.
So my final conclusion is: When you change stocks in the manufacturing central you need to set and save per rule. (if you change more then one rules and save them, only one change is calculated in the end product).
I hope this is clear. (I tested this with version 1.7.2, on a clone of the website with only Woocommerce and ATUM plugins activated.