Make sure that particular user does not own any other files as well. Sometimes ownership gets screwed up on these Cpanel servers and a user will end up owning files outside their home directory, which will cause your quota to report the wrong utilization.
Try typing &quota USER& changing USER for the actual username. This will show you how many files are owned by the user in which partitions and the amount of space being used. You can then correct the ownership of the screwed up files.
Try typing &quota USER& changing USER for the actual username. This will show you how many files are owned by the user in which partitions and the amount of space being used. You can then correct the ownership of the screwed up files.