If your cpanel is showing wrong mailbox quota than the actual usage
You need to Do the following steps to get it fixed.
Login to your server with root user and check the actual usage of email account
#cd /home/username/mail/domain.rld /
#du -sch emailaccount
If you found the difference in actual usage and cpanel results then
# rm -f maildirsize
Now login to your cpanel >> email >> email account option > Reset Quota and reset the quota of the account.