Default Domain Policy / Computer Configuration / Policies / Windows Settings / Local Policies / User Rights Assignment
Should be configured in the Default Domain Controller Policy instead. You will most likely need to keep this setting in the Default Domain policy now that you have configured it. That will be easier than trying to reconfigure
the computers back to the defaults.
Default Domain Policy / Computer Configuration / Policies / Windows Settings / Security Settings / System Services
I'm not sure this is even needed, but given that you have mucked around with these settings, its going to be very hard to tell with out a lot of research on your part. In general use the
Default Domain Controller Policy instead. I would reconfigure the Default Domain policy back to its defaults if possible on this one.
I would consider builting a test domain from scratch and compare the known default settings in that domain to your existing domain and work on correctly configuring your original domain back to the defautls if at all possible.
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