In the past, that would be caused by attempting to create a backup while logged into the cPanel interface using the reseller override feature. Since the reseller had no access to the database, the resulting backup file was much smaller than it should have been.
In the latest versions of cPanel/WHM, the interface will notify you about this situation (if logged in using reseller override) before you generate a bad backup. However, this condition also prevents access to phpMyAdmin via cPanel.
Are you accessing phpMyAdmin via cPanel or via WHM?