Group Policies are being applied to the system and can be confirmed using vgptool, but some settings are incomplete or not applying from one Group Policy Object (GPO) to the next.
The GPO version is not updating correctly in Active Directory (AD).
Vgptool will download and apply GPO settings when it sees that the GPO version information has changed in AD. If changes are made to the GPO in AD, but the version doesn't change, vgptool will not know there is a change, and thus will not apply the updated GPO.
Confirm that permissions on the GPO are correct and will allow for the version to update.