It seems that the quota displayed on some of my VDS is different than when I right click the VDS's directory and view the quota of the directory.
In some of the cases where the quota that Sphera shows is higher than what you see when right clicking the directory and looking at the size, the problem might be that there are files that are owned by the VDS owner however the files have been deleted to the recycling bin and are still being calculated by the quota service as belonging to the VDS. You can delete the files from the recycling bin in order to overcome this issue.
In cases where Sphera shows lower quota than what the VDS directory shows, it seems that the Admin user of the server has uploaded or created some files for the user and therefore there are files under the VDS directory owned by Administrator and not by the VDS owner which causes you to see the quota on the directory but sphera does not calculate this as the VDSs quota.
In order to change the user you can use a utility called SunInAcl from the windows resource kit.