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If the site does impose pop-up windows this only happen once.
Saves the user from displaying the same secondary windows repeatedly and minimizes the number of window closing actions.
When a pop-up is generated it send a cookie which tags the page as having been seen by the user. However it is preferable never to use pop-ups which are often blocked by user agents are badly perceived by users and are not really very efficient.
In the case of pop-ups being used, check that they only appear once and not on reloading a page.