I decided to check my scheduled backups log and found it was failing. I get this error on the first domain.
Dumping MySQL database webmaste_xenforo .. .. dump failed! mysqldump: Got error: 1045: Access denied for user 'root'@'localhost' (using password: YES) when trying to connect
Tried a manual backup and got the same problem. Tried backing up a different server, got the same error. I have edited my my.cnf recently, maybe I removed something I shouldn't have?