When I check the status of my email systems (using the mailboxes.domain.com), it says I have 42MB of mail, but using both the webmail and the normal POP mail services, all folders are empty, including old mailboxes, etc. Mail readers are set to remove mail when downloaded. Curious as to whether stuff is really being stored or whether this is some kind of craziness of the system.
I guess some old files are still cached in your email box. You can try to delete the email address and re-create it. If you do not want to disturb the service of your email address, I think the only way to ask DH support to take a look.
I looked again at the email setup in the control panel and it seems that the website files count against this address (there’s a footnote that I missed). DH support confirmed that was the source of the ‘problem’. Worth noting that if you set the email box size limit smallish (say 100MB) it can get used up quite quickly with web files. I have now removed the limit as suggested by support.