Ah ok, we do this all the time with captivate. Make a chapter called popups or something like that. In that chapter add each SWF file generated from captivate to a different page. Next, when you need to launch that page, create a button, then add this action:
On Click
Action: Go To Page
Target: Page in Popup
Then choose open in a new window. Customize the properties of the window.
That should do it.
P.S. Purdue is going to beat Illinois on 10/24 :)