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What you can do is amend the script such that it only opens a popup window approx. every one in nth times, by adding a random number:
<script language="JavaScript"><!-- var nth = 10; var rnd = Math.floor(Math.random() * nth) + 1; if (rnd == nth) { var windowHandle = window.open('popup.htm','windowName','width=400,height=400'); } //--></script>