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Things I know, is that they can tell if your site in general has LOTS of popups, and might have some percentage penalty. not sure if google or any se uses that, but I know if you look up a domain on alexa.com is can tell you the percentage of the site that pages have popups
What i do know is that sites with alot of javascript in the top of their pages (as well as the very BOTTOM) will NOT rank well,
I was able to get alot better results including the javascript in an external .js file
and loading that with a one liner in the html
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