Domain mapping manipulating Permalinks


We are developing a website which uses the sub-folder multisite structure, etc..

What we need is domain mapping so that some sites can be mapped to a domain name - however when I enable this, the permalink editor in the admin strips the sub-folder off.

So where I previously had Permalink: it now shows as and clicking on 'View Post' it takes me to a 404 page.

It is definitely being caused by the Domain Mapping as when I turn it off it works fine.

Here is an example image I have made: