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[edited by: tedster at 11:57 pm (utc) on April 22, 2003]
The document that loads into your new window should contain your Flash movie and probably the "skip intro" button as well.
Pop-up windows tend to annoy users. So do flash intros.
Combining the two seems like a bad idea. :)
If users have to sit through the same intro everytime that they come to your site then they will soon get very bored with it (no matter how cool it is).
You could look at using a cookie - if the user has been to your site once, skip the flash intro and bring them straight to the content.