Right. This is getting weirder and weirder. I added a base tag like so:
<head>
<base href="[(site_url)]" />
This doesn’t make the javascript work. It does, however, totally stop my site from being displayed in IE.

When browsing to my url it says something like:
The site www.etc can’t be opened. The operation is being terminated
In Firefox everything is fine. The base tag in the source looks like this:
<base href="http://www.arlingenarling.com/nieuw/" />
I think that’s ok.
I guess this is a server issue, then? I’ve never seen this before...