Hello all.
I am also having this problem on my mail server.  This is pretty much a base install, no add-ons other than Backup2WS.  It has never been moved from machine to machine, etc.  No drama, no history.
I have one user who's quota report is far in excess of the actual files that belong to her on the system.
Result of "quota -v ACCOUNTNAME:
Disk quotas for user ACCOUNTNAME (uid 5044):
     Filesystem  blocks   quota   limit   grace   files   quota   limit   grace
/dev/mapper/vg_primary-lv_root
                 916944  921600 1024000            4518       0       0
This matches the report in the server manager panel
When I run the command:
find / -user 5044 > /tmp/reportfile
The resulting file contains just 2,495 files, which total to about 406 MB in size.  This is just over 1/2 the size and number of files reported by quota.  I've scanned /etc/passwd and find no weirdness on uid 5044 or ACCOUNTNAME (both occur on one, and only one line in the file):
ACCOUNTNAME:x:5044:5044:USER NAME:/home/e-smith/files/users/ACCOUNTNAME:/usr/bin/rssh
I'm stumped.  Anyone have any ideas why this is happening, or what else I can check?
This is version 7.4 btw.