It appears that many Zen Cart shops have a configuration table entry like this:
(1018, 'Installed Modules', '', '', 'This is automatically updated. No need to edit.', 6, 0, NULL, '2008-03-07 11:51:49', NULL, NULL),
This is the offending empty configuration_key that results in a duplicate configuration_key error message (when using the sql patch tool, and under certain circumstances). Normally the 'Installed Modules' key would be MODULE_SHIPPING_INSTALLED, MODULE_ORDER_TOTAL_INSTALLED or MODULE_PAYMENT_INSTALLED. Maybe there are more? No idea how and when the empty key is added to the configuration table. Most shops don't have it.