The permissions on the mailboxes are changed when the email is accessed through CPanel. There were several on the CPanel forums that had experienced it as well but no one had a fix.
If you run /scripts/mailperm you might very well see some boxes being repaired. Boxes you didn't know were broke in the first place. I ran into this because of a problem with a client not receiving email. I checked the permissions and they were wrong. I repaired them thinking it was a fluke, like 45 minutes later same problem. Permissions were changed, this time I repaired them again, checked the email via CPanel and then checked the permissions. They were wrong again!
I had to set up a Cron to keep on top of it. It reoccurs a lot! There was no official fix at CPanel so I was wondering if anyone had run into this yet and if so what they did to correct it other than setting up a Cron...