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Is there anyone help me running popup pages even if popup stopper is there.
Negative.
Moreover how many internet users are using popup stopper now a days?
Depends on what your target market is - webmasters; probably most of them, students; probably very few...
To be honest, more and more service providers (AOL et all) are offering to automatically stop pop-ups at the connection level - it is a dying medium. Perhaps you could consider other types of advertising/displaying content.