I'm running Windows 7 Professional 64-bit and having the same problem. You can easily resolve the "Hidden File" problem by right clicking on the file, select Properties, and remove the check box next to "Hidden". If you tagged all the photos in a folder, simply select all (ctrl-A) and do the same. It solved the hidden file problem for me without having to show all hidden files.
The problem I'm running into that I can't fix is that even after doing this, Carbonite now recognizes these files as system files and refuses to back them up. Even if you try to manually force Carbonite to back them up, it immediately unselects the check box. Hopefully somebody knows of a solution.
It's weird, because I was tagging photos just a few weeks ago, and didn't have any problems at all. I don't know if there was an update at some point that screwed this all up.