That is very odd that you would get the same SQL error (I assume you mean duplicate key 999) since the SQL if executed properly deletes this key?

Code:
DELETE FROM configuration where configuration_group_id = '999';
Can you clarify this?

Also, when you say:
still no options in the configuration tool
Are you saying the Configuration->User Tracking Config menu choice is missing?

-or-

Do you mean when you select Configuration->User Tracking Config there are not six configuration switches listed?

Let me know and I will help?

Jeff