When I change the code generation settings in one configuration, it also changes in others. Why?

How a code is generated in Autogenerated Code Lists is stored in the code list itself. The settings could be discount value, expiry, prefix, etc. 

This means that if you have the same code list in multiple configurations, changing the settings in one will also be reflected in the other configuration.
If you need to have different code generation settings for different configurations you need to create separate code lists which each have their own code generation settings.
You can create a new code list by going to the "Code lists" tab:

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