User Configuration will only be applied if the GPO is linked at or above the Organizational Unit (OU) or Container where the User account you're testing with is located. If, for example, the Computer account is located in a "Servers" OU where you've linked your "CIS Recommendations" GPO, but the user account you're logging-on with is located in, say, the default "Users" container, those User Configuration settings in the "CIS Recommendations" GPO wouldn't apply.
I'd recommend reading-up on Group Policy application in general. Understanding how settings are applied based on the location of GPO links and the OUs where Computer and User account objects are located is going to be helpful to you. There are a variety of different resources you might consult. Some ideas include:
Group Policy Basics – Part 1: Understanding the Structure of a Group Policy Object
Group Policy Basics – Part 2: Understanding Which GPOs to Apply
Group Policy Basics – Part 3: How Clients Process GPOs
The specific setting you're looking for, if you do want to place User Configuration settings in a GPO linked in a place that would typically apply only to Computer accounts is Loopback Policy Processing. This functionality allows the User Configuration settings in GPOs that apply to the Computer to be either merged with, or out-right replace the User Configuration settings that would normally be applied to a given User account logging-on to that Computer.