If a cPanel email user quota does not match what is being reported by the system or a mail client run the following to determine how much space has been used for real:

du -hs /home/username/mail/userdomain.com/user/

then compare it with what cPanel reports for the disk usage, if they are different delete:

/home/username/mail/domain.com/user/maildirsize

finally re-login to cPanel and it should be resolved.