From what I can tell, the option is under "customers", not "configuration".
Oh wait ... you were looking for settings.... duh....
It's possible that the various SQL statements you ran didn't complete properly ... namely:
-- Purchase Order payment module configs
INSERT INTO configuration VALUES (NULL, 'Enable Purchase Order Module', 'MODULE_PAYMENT_PURCHASE_ORDER_STATUS', 'True', 'Do you want to accept Purchase Order payments?', 6, 1, now(), now(), NULL, 'zen_cfg_select_option(array(''True'', ''False''), ');
INSERT INTO configuration VALUES (NULL, 'Make payable to:', 'MODULE_PAYMENT_PURCHASE_ORDER_PAYTO', 'Destination ImagiNation, Inc.', 'Who should payments be made payable to?', 6, 2, now(), now(), NULL, NULL);
INSERT INTO configuration VALUES (NULL, 'Sort order of display.', 'MODULE_PAYMENT_PURCHASE_ORDER_SORT_ORDER', '0', 'Sort order of display. Lowest is displayed first.', 6, 4, now(), now(), NULL, NULL);
INSERT INTO configuration VALUES (NULL, 'Payment Zone', 'MODULE_PAYMENT_PURCHASE_ORDER_ZONE', '0', 'If a zone is selected, only enable this payment method for that zone.', 6, 5, now(), now(), 'zen_get_zone_class_title', 'zen_cfg_pull_down_zone_classes(');
INSERT INTO configuration VALUES (NULL, 'Set Order Status', 'MODULE_PAYMENT_PURCHASE_ORDER_ORDER_STATUS_ID', '2', 'Set the status of orders made with this payment module to this value', 6, 6, now(), now(), 'zen_get_order_status_name', 'zen_cfg_pull_down_order_statuses(');
-- Super Orders configuration group
INSERT INTO `configuration_group` VALUES (28, 'Super Orders', 'Settings for Super Order features', 100, 1);
-- Super Orders configs (Admin > Configuration > Super Orders)
-- Automatic Status Updating
INSERT INTO `configuration` VALUES ('', 'Auto Status - Purchase Order', 'AUTO_STATUS_PO', '2', 'Number of the status assigned to an order when a purchase order is added to the payment data.', 28, 11, now(), now(), 'zen_get_order_status_name', 'zen_cfg_pull_down_order_statuses(');
INSERT INTO `configuration` VALUES ('', 'Auto Status - Payment', 'AUTO_STATUS_PAYMENT', '2', 'Number of the order status assigned when a payment (<B>not</B> attached to a purchase order) is added to the payment data.', 28, 10, now(), now(), 'zen_get_order_status_name', 'zen_cfg_pull_down_order_statuses(');
INSERT INTO `configuration` VALUES ('', 'Auto Status - P.O. Payment', 'AUTO_STATUS_PO_PAYMENT', '2', 'Number of the order status assigned when a payment <B>attached to a purchase order</B> is added to the payment data.', 28, 10, now(), now(), 'zen_get_order_status_name', 'zen_cfg_pull_down_order_statuses(');
INSERT INTO `configuration` VALUES ('', 'Auto Status - Refund', 'AUTO_STATUS_REFUND', '2', 'Number of the order status assigned when a refund is added to the payment data.', 28, 13, now(), now(), 'zen_get_order_status_name', 'zen_cfg_pull_down_order_statuses(');
INSERT INTO `configuration` VALUES ('', 'Auto Comments - Payment', 'AUTO_COMMENTS_PAYMENT', 'Payment received in our office. Payment ID: %s', 'You''ll have the option of adding these pre-configured comments to an order when a payment is entered. You can attach the payment number to the comments by typing <b>%s</b>.', 28, 14, now(), now(), NULL, NULL);
INSERT INTO `configuration` VALUES ('', 'Auto Comments - P.O. Payment', 'AUTO_COMMENTS_PO_PAYMENT', 'Payment on purchase order received in our office. Payment ID: %s', 'You''ll have the option of adding these pre-configured comments to an order when a purchase order payment is entered. You can attach the payment number to the comments by typing <b>%s</b>.', 28, 14, now(), now(), NULL, NULL);
INSERT INTO `configuration` VALUES ('', 'Auto Comments - Purchase Order', 'AUTO_COMMENTS_PO', 'Purchase Order #%s received in our office', 'You''ll have the option of adding these pre-configured comments to an order when a purchase order is entered. You can attach the payment number to the comments by typing <b>%s</b>.', 28, 15, now(), now(), NULL, NULL);
INSERT INTO `configuration` VALUES ('', 'Auto Comments - Refund', 'AUTO_COMMENTS_REFUND', 'Refund #%s has been issued from our office.', 'You''ll have the option of adding these pre-configured comments to an order when a refund is entered. You can attach the refund number to the comments by typing <b>%s</b>.', 28, 17, now(), now(), NULL, NULL);
INSERT INTO `configuration` VALUES ('', 'Federal Tax Exempt Number', 'FED_TAX_ID_NUMBER', '00-000000', 'If your tax exempt, then you should have a federal tax ID number. Enter the number here and the tax columns will not appear on the invoice. The number will also be displayed at the top of the invoice.', 28, 50, now(), now(), NULL , NULL);
INSERT INTO `configuration` VALUES ('', 'Closed Status - "Cancelled"', 'STATUS_ORDER_CANCELLED', '0', 'Insert the order status ID # you would like to assign to an order when you press the special "Cancelled!" button on super_orders.php.<p>If you do not have a "cancel" status, or do not want assign one automatically, choose <B>default</B> and this option will be ignored.<p><strong>You cannot attach comments or notify the customer using this option.</strong>', 28, 30, now(), now(), 'zen_get_order_status_name', 'zen_cfg_pull_down_order_statuses(');
INSERT INTO `configuration` VALUES ('', 'Closed Status - "Completed"', 'STATUS_ORDER_COMPLETED', '0', 'Insert the order status ID # you would like to assign to an order when you press the special "Completed!" button on super_orders.php.<p>If you do not have a "complete" status, or do not want assign one automatically, choose <B>default</B> and this option will be ignored.<p><strong>You cannot attach comments or notify the customer using this option.</strong>', 28, 30, now(), now(), 'zen_get_order_status_name', 'zen_cfg_pull_down_order_statuses(');
INSERT INTO `configuration` VALUES ('', 'Closed Status - "Reopened"', 'STATUS_ORDER_REOPEN', '0', 'Insert the order status ID # you would like to assign to an order when you undo an order\'s cancelled/completed status.<p>If you do not have a "reopened" status, or do not want assign one automatically, choose <B>default</B> and this option will be ignored.<p><strong>You cannot attach comments or notify the customer using this option.</strong>', 28, 30, now(), now(), 'zen_get_order_status_name', 'zen_cfg_pull_down_order_statuses(');
