Thought I best report this:

Moved a site to a new server running Aegir, the rotating banner stopped working. So I asked the hosting Company if they could offer an explanation, Here's the answer:

This is expected. Our configuration doesn't support
any php files in themes.

By the way, it should never be used. Any image rotation
etc should be handled via javascript, so it is a bad practice
in the theme design, as images should never be served
via php (unless for imagecache module)