Okay, I figured out what my problem was.
I had some failed backups from yesterday, when I tried to get hardlinking working (and I also had a permission issue with the MySQL dump). As of such, I cleared the backup disk manually, and then triggered a backup cleanup in the Cloudron UI. Then I tried to back up again, however, I believe that Cloudron keeps an index of files it has already backed up to keep things speedy (which is nice). As of such, even though the other files no longer existed, it was only backing up the changes.
To solve it, I just changed the backup method to a different method, and then changed it back again, which cleared the index.
Thanks for all your help on this :).