You run the Configuration Wizard tool (ConfigurationWizard.exe). When you click Network Integration, and then click Advanced to enable or disable each IP protocol, the IP protocols are saved as you want. However, when you close and then reopen the configuration tool, every IP protocols is enabled regardless of its previous setting.
This problem is fixed in Cumulative Update 1 for Host Integration Server 2016.
Microsoft has confirmed that this is a problem in the Microsoft products that are listed in the "Applies to" section.
Learn about the terminology Microsoft uses to describe software updates.