Files in /files Dir Not Working?

I have no idea what just changed, but all of a sudden .css and .jpg files in the /files and /site.com/files directories are simply not loading.

I can access them from the shell, and I have checked their permissions. I have triple checked the html (both generated by me, and by drupal) in the source, and nothing, absolutely nothing, looks wrong.

Pictures don't show up and css rules fail to load (both pics and css were very normal yesterday).

Im at a complete loss. Does anyone have any suggestions where to look?

Many thanks

PS:Yes, cleared cache on drupal and locally.