On cPanel server , sometimes disk quota are not displayed correctly. The reason is that the " second level quota " is not enabled on Node.
All you need to do is connect to the root of OpenVZ node where the VPS is hosted .
You can enable second level quota by simply setting up a value for " quotaugidlimit " parameter.
This is quite simple and can be done using following commands from the node -
Note : Replace the number 123 with CTID (Server ID) of your VPS.
vzctl stop 123
vzctl set 123 --quotaugidlimit 10000 --setmod restart --save
vzctl start 123
vzctl set 123 --quotaugidlimit 10000 --setmod restart --save
vzctl start 123
You can then login to your VPS and run command /scripts/fixquotas to fix any quota related issue.
Thereafter, login to the WHM Panel and list the accounts and you will notice that disk values are updated properly.