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So here's the thing about pops. You must code them right and place limits on them for them not to effect your SEO. If you do it right, then you will not have any problems.
Setting up trigger elements on the pops is important. Google will warn you about it in Google Webmaster Tools about pops triggering on Chrome when they are not suppose to show. Like when someone clicks on a blank background and etc.
Limiting pops is important too. Running them too many times per day may reduce time on site so be mindful of that. Also running quality ads is important as well.
We help our publishers with the setting up of our code because each site is different. Most of our pubs use KVS or Mechbunny so we already have the trigger elements ready to go for pubs using those templates. So far so good on our script being Google complaint and not affecting SEO.
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