Do you have delegated the user registration to some special users? Does these special users sometimes create user with a pop3 mailsystem instead the in the registration policy configured Lotus Notes mailsystem? Or do they sometimes choose the wrong server when they create a mailfile (and you see that the user has a mailfile on your sametime or application server)? Or do they change some other parts which you set as default in your registration policy?
Then vote for a registration policy lockdown feature. Similar to the desktop policy I would like to prevent this special user from changing some options (which I define in the policy document) with this policy.