Came across this issue at work where a client was receiving this message when trying to enter webmail, even though the e-mail account and cPanel account were not over quota.
Internal Server Error
User ‘useraccount’ is over quota.
This happens when the users ‘overquota’ status is cached and can be fixed by removing the users folder located at the following.
/var/cpanel/overquota/username
Awesome post! It really helped me a lot! Thanks for sharing it.