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At worst having interstitial ads will seriously hack off real visitors and they'll never visit your site again.
Depending on how the links are done, search engines won't even know about the popup because they don't trigger JS which is the way most interstitials are done.
Giving an example of the code (or a URI) will get you a better answer, because right now I'm merely surmising how it's set up.
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Chris. ->> Links are advertising NOT optimising!! <<-
A foolish consistency is the hobgoblin of little minds
Thought for today:- I SEO the only industry where all the cowboys are Indians?
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