Since the disk usage is broke and has been forever then the quota system is pointless as well
Have an account with quota of 500 mb - disk usage and quota ONLY see space in public_html
this user was at 505 mb - as I began to poke around the new file manager showed me that he also had a old.public_html folder that was also using 500+ mb of space
so file manager see the right file sizes BUT quota and cpanel only see the data in public_html
in this case user was using over 2.5 x quota
Doug
I would recommend submitting a support ticket regarding this issue. Typically all files owned by a user will be counted towards their disk quota, which obviously is not happening in your situation.