Applications and Preferences added at the Group Policy level are not applying.
Forcing a group policy update and logging off and on and running slgpo.exe in the SecureLogin directory force the GPO to applied to the user.
As per Microsoft standards, GPO's have their own inheritance model. You should ensure the preferences you are applying are not being superseded by other GPO's.Add preferences using the "top most" GPO down, and set them to Yes and No instead of leaving them to Default to avoid confusion. Alternatively, preferences could be added using the OU structure, and applications and password policies could be added via GPO, if desired.