Domain mapping manipulating Permalinks

Hi,

We are developing a website which uses the sub-folder multisite structure example.com, example.com/site2/ example.com/site3/ 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: http://example.com/site2/the-permalink/ it now shows as http://example.com/the-permalink/ 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:

http://i.imgur.com/3CzCHS6.jpg

Thanks,
Chris.