You might think that's obvious, but you'd be wrong. Software publishers were cracking down on duplicating manuals as a means of trying to curb software piracy.
I can practically guarantee that the "obstinate employee" was given clear direction by their manager on the subject.
Though you do have to keep in mind that depending on when exactly this happened, Kinko's might still have been a collection of hundreds of largely autonomous regional partnerships, each of which could set their own policy.