I found someone else with the same problem, editing the web.config file as per below seemed to fix it.
<rule name=”WordPress Rule 5″ stopProcessing=”true”>
<match url=”^[_0-9a-zA-Z-]+/(wp-(content|admin|includes).*)” ignoreCase=”false” />
<action type=”Rewrite” url=”{R:1}” />
</rule>
Does anyone know if there are any other mods I should be making to the web.config?
cheers!