Well, I was going to suggest that the email could be in a spam, trash, or even sent folder, or some other folder there.
You could always manually check from the command line where the usage is coming from.
If you log in over SSH, and go into the users home directory (something like /home/VIRTUAL_SERVER_OWNER/homes/EMAIL_USER/Maildir), and you type “ls -a”, you’ll see a list of all the IMAP folder (the directories starting with a . character).
So, to check how much disk space the spam folder is using, you could type:
du -sh .spam
Hopefully that’ll help you track down where the usage is
-Eric
So, generally Linux disk quotas don’t make up numbers. There are very likely files located somewhere on that partition that consume 50MB.
find /home -user username
Will show you if there are any files you don’t know about somewhere in /home (note that if you only have /, you could also have files in /var and /tmp, and maybe even other places, owned by the user…and they also consume quota). So, if / is the partition where folks live and where quotas are applied you need to look there, too.