It is very simple - if you copy and paste a factory, the setting of what the copied factory is building doesn't show up in the pasted factory.
When setting up a factory complex, this bug becomes tremendously frustrating. :) I understand there are plans to make factory settings similar to rail settings, but sure would appreciate fixing of what I imagine is a bug until the overhaul happens. :)
Interestingly enough, copy and paste of a cargo chest DOES retain the auto-pull info, which I think is somewhat similar, maybe not.
Thank you!