Well done! The relative pronoun is tricky. Here, you can't use "which" because you are referring to a person, "user". The preposition you need here is "under", for reasons I don't understand :-(
"Grant privileges to the user account under which Windows services have been installed."
You will also hear/read it this way:
"Grant privileges to the user under whose account Windows services have been installed." (However, technically you are not installing under a user, but under a user's account.)