GPO for user config not applying

[krosbonz]

Here is our situation;

We have a GPO that contains only user configuration. Specifically, it has a list of sites to be put in Trusted Sites in IE.
This GPO has been applied at the top leve of our User OU which contains any number of sub-OUs all containing user accounts.
There is no Block Enheritance set on the top level OU or any sub-OUs.

The GPO not only doesn't get applied, but if you run a RSOP (gpresult /R) it doesn't show up at all. Blocked or applied.

I have created a test out and put individual user accounts in this OU and applied the GPO directly to the test OU, but it still will not apply or show up when I run a RSOP.
If I go into Group Policy Management and run Group Policy Results for the test user account the GPO is not listed.
If I use Group Policy Modeling the GPO is listed.

The scope of the GPO is Authenticated Users
Authenticated users are delegated Read and Apply GPO

The only way I have been able to get this policy to show up with RSOP and apply is to move the computer account the user account is logging into into the same OU as the user account where the GPO is linked.

I have no idea why this is the case or how to fix it.