Oh man, I am an idiot. I just realized I was updating everything in the admin/sources directory locally with my web editor and then uploading with it. I completely forgot about that very strange feature of CC to copy and rename the admin folder on the server with a random _xxxxx to obscure the login page from bots. I do see the purpose, but it is kind of an oddity that I have never seen before and still can't get used to it in my workflow. I need to remember to push the modified admin folder back to my local site files after upgrades (or at least rename it the same) so it syncs with the right folder. I fixed THAT one and it is now working.
Thanks for your time on this. Sorry it was a wild goose chase.