Yes it is, but the headinclude edited is for that style.

So it's not picking up that it's the CMS page.

Can we get a link to the site?

Sorry as mentioned this is only on a dev server locally at the moment.

I'm pretty sure vbcms (e.g. content.php) doesn't include the code added to the header.

Is THIS_SCRIPT == 'vbcms' correct?

In the ACP under Settings -> Options -> General Settings there's "Add Template Name in HTML Comments", which will let you view the html source and see which templates are included. I have pretty much the default 4.1.3 install and the main page (content.php) includes the headinclude template. I suppose it's possible that yours doesn't for some reason. And like Lynne said, you can have a different one for each style so you could have edited a headinclude but not the right one.

In any case, content.php contains "define('THIS_SCRIPT', 'vbcms');", so the problem should be that your popup appears on every content.php page and not just the home page.