Website(s) transferred to new machine: problems with application root (IIS7)

I've just transferred the websites on my old development machine to my new one using the Web Deployment Tool (which did Ok but didn't work perfectly).

I'm starting work on one of the web application that runs off the root of the Default Web Site. Seemed to be running OK at first but I'm adding some links in to images in a couple of location (one set in application subdir, another in a virtual directory below the application), but I'm having a problem where a relative path (i.e. /images/myimage.png) is not being linked in correctly:

Rendered url should be:

//MyServer/MySite/Images/MyImage.png

Actually rendered as:

//MyServer/Images/MyImage.png

It is as if the server doesn't recognise the application, but the application is configured as an application and the Global.asa is being read (i.e. DB connections, application variables etc)

I'm guess that this is a quirk of the Web Deployment Tool... Anyone any idea what I need to do to achieve the expected behaviour?