Images Not Uploading on Domain Mapped Site

I have a domain mapped site that images are suddenly not visible, both in the media gallery and live.

When I try to upload a new image to it doesnt show either. When I test it on a non-domain mapped site, there is no problem.

The 2 sites create 2 different image url structures as follows:

non-domain mapped:
http://domain.com/wp-content/uploads/2013/09/image.jpg

Domain Mapped site:
http://subdomain.domain.com/files/2013/09/image.jpg

The domain mapped site has been live for over 9 months. Its only now that I've noticed a problem. Perhaps after a recent plugin upgrade.

Any ideas why this could be happening?

thanks
Paul