Chaituu - I'm not sure I understand 100% the issue, but my recommendation based on your description is to create the Popup window directly within Flash. Assuming that your Flash component already covers the area that you want to have the popup window in, this is a better way to go, avoids potential browser bugs, saves you having to deal with Flash' ExternalInterface and JavaScript, and makes it simple to create a chromeless window.
You can also then do cool things like blur out the background or put a transparent overlay over inactive elements.
Of course, this would require a little bit of programming in Flash - Im assuming you have those resources already because you're going to be triggering these popups from within Flash.
If you need more help, please post some specifics about how you want the popup to work.
Regards,
Tom