The issue is with the odd named files and folders that have been uploaded. I couldn't even delete them through Dreamweaver, and when I downloaded them they don't even show up in windows explorer.
I renamed the files directory to files_old and I'm re-uploading all of the files that appear in windows and it appears to be working again.
I've also uploaded a new file manager for your contents update page. If you like it you can copy over the line on the update page and use it on the insert page as well. You can see the line I added at line 409 of the contents_update.php page and the line I commented out below. It may do better preventing uploading and naming of folders that cause issues.