HKLM\Software\Policies registry entries must be managed by GPO ONLY.
https://technet.microsoft.com/en-us/library/cc939918.aspx
“The Policies subkey contains entries that store Group Policy settings. Group Policy adds, deletes, and changes the values of entries in this subkey when you use the Group Policy snap-in to enable or disable a policy. When the policies affecting a particular user or computer change, such as when the user moves to a new user group, Group Policy deletes the entries for the old group and adds the entries for the new group.”
Group Policy manages registry entries in mainly 2 Policies subkeys:
- HKLM\SOFTWARE\Policies
- HKCU\SOFTWARE\Policies
“Do not use a registry editor to change the values of entries in this subkey. If you do, they will be overwritten the next time the policies are refreshed.”
So, these registry entries must not be modified by an installation package, only GPO.