I believe Javascript to serve AdSense is to be used only by the premium publishers, not by us riff-raff. If he's using Javascript to serve the ads and has not been invited to be a premium publisher, that in itself might be part of the problem. If you Google discussions of the specific message he is asking about, it ONLY applies to premium publishers using Javascript. <iframe> ads are supposed to handle the skipping automatically.
Ok, now I'm REALLY confused.
When I look at one of my ad units and click "get code", this is what I get (and what I assume people mean when referring to javascript):
<script type="text/javascript"><!--
google_ad_client = "ca-pub-xxxx";
/* Last Read Post */
google_ad_slot = "xxxxx";
google_ad_width = 728;
google_ad_height = 90;
//-->
</script><script type="text/javascript"
src="http://pagead2.googlesyndication.com/pagead/show_ads.js"></script>
I thought that Adsense stopped using iframes years ago?