No, they're in the right directory. But you got me thinking, is there a file that tells the installation it's not upgraded? Essentially what I did, to save time, was move my .htaccess, custom style folder, and library/config.php file out, backed up all the other stuff, and copied the RC2 files from another folder, and then replaced all my unique stuff.
My FTP program (Transmit 4 on mac) is a pain with XF upgrades. It really takes forever to upgrade XF.
If I tell it to replace my styles folder, it will literally replace it (deleting my custom style folder). Same thing with the library folder and config.php. It will delete config.php in the process of "replacing" the library folder.
I still don't understand why the installation identifies itself as Beta 6 with the RC2 files, though (for upgrade purposes).
Furthermore, I haven't had this problem before, so I'm not sure what's going on.
You see, I've been changing servers the past few days... and I thought I had pointed my forum's domain over to the new server... and was operating on that assumption when I went to the URL. Since I hadn't made any other changes, I figured I was good. Didn't ping the domain to check the IP it was on (duhrrrrrr). Once I actually pointed the domain at the new server, it was fine (and, for the record, what I did would have worked ;P)
So, thank you guys for the help (and the very useful Transmit tips).