Look at table 'og_config_categories', and look for the registry with column 'name' = 'modules', it must have the property 'is_system' = 0.
if it isn't there run this in your database
INSERT INTO `og_config_categories` (`name`, `is_system`, `category_order`) VALUES ('modules', 0, 3) ON DUPLICATE KEY UPDATE id=id;
Same thing at table 'og_administration_tools'. There should be only two registries, named 'test_mail_settings' and 'mass_mailer'
if they are not there, run this
INSERT INTO `og_administration_tools` (`name`, `controller`, `action`, `order`) VALUES
('test_mail_settings', 'administration', 'tool_test_email', 1),
('mass_mailer', 'administration', 'tool_mass_mailer', 2);
hope this helps