Is this a virtual server? If yes, then it might be that the harddisk usage can not be displayed, as the Linux "repquota -avug" command does not display it under OpenVZ.
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I have had sites de-activate when over their quota so ISPConfig3 knows that a site is over quota it just doesn't display them.
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Here you mix up traffic quota with harddisk quota. Deactivate a website is for traffic quota and not harddisk quota.