Tried inserting 'fullscreen' to the third parameter string of window.open(), and it worked - the popup opens fullscreen.
The problem is, there's no way to resize or close the window (at least in IE6). In fact the only way out of the problem was by pressing the Windows key to bring up the bottom toolbar - still can't close the popup though.
Is it because I'm linking direct to a flash file rather than a html page? Or have I just discovered a new way for those people who write advertising popup windows to annoy the rest of us with an unignorable popup?