I’m going back to my initial idea and dare to say it’s a caching problem. Caching plugins use very complex algorithms and occasionally they fall into a loophole and just stop working properly. In situations like this actions like clearing cache and deactivating the plugin don’t work as expected. Since the problem is more than one week old and caching plugins usually clean their cache at least once a week I believe it’s stuck somewhere and serving stalled content.
I never used WP Super Cache but I know that W3 Total Cache installs some drop-in scripts that reside outside the plugin and keep working even if you delete the plugin. It happened to me several times that I needed to manually delete those drop-ins and the disk cache and even reboot the server. Usually that happened when updating WordPress and updating the database was stuck in an infinite loop.
I suggest you search all files that the caching plugin created and delete them. Then if you have the possibility I recommend to reboot the server. I also recommend you install a database maintenance plugin and check your database for any errors and perform a cleanup. You can try any of these: