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Wayfarer has AdBlock Plus files support and pop up windows are blocked by default. That said, ad blocking is never perfect and may be out of date or the supplied file is not targeting the websites you are visiting. Hard to say more since you have not actually provided a link...

Wayfarer's Resources directory contains an easylist.dat file. You can place a file named easylist.txt in the same directory and delete the .dat file to force a refresh (Wayfarer will take about 2 minutes to start the next time you run it!).