We note some of the potential reasons for disk space usage discrepancies on our Disk Usage document. As a website owner without root access, the troubleshooting options available to you for this particular issue are limited.
I recommend reporting this issue to your web hosting provider so they can take a closer look.
I remember there was a thread about Disk Quota issues that CPanel has been trying to fix. I was subscribed to that but couldn't find it somehow. Was that fixed? We're still having the same issue where accounts disk usage isn't read properly by the server. Also, the issue with "Other Usage" still exist. Kindly help. Thanks.