The CMS, privileges, theme customization, etc. was all working like it was supposed to. A few days ago, I was uploading files via the FTP, and I simultaneously uploaded an image with the CMS. Didn't think that through. Anyway, it is now not populating the site with the pages correctly, is not including background images from the CSS, and will not allow me to build the database.
Okay - we are one step closer. I had checked all the files, but the paths are still not working. It seems to not be updating the layout.css, no matter what kind of flush I do (?flush=1, ?flush=all, db/build?flush=1, images/flush.