HELPPPPPPP Urgent problem - Points Reward

I need urgent help with a current problem.

I am running a wordpress multisite, with buddypress, and multi-db

Everything was working great and i was ready for launch tommorow.

I did a test registration and there is now a major issue.

When a user registers the following happens:

1: They receive 2 emails for 2 different activiation addresses. 1 with the main site apended and the second with there blog url apended.

2: Regardless of which activation email you click it makes no difference but then you are given the password even though this was chosen on signup.

3: Even you activate your account when i go to the main blog there site doesnt show up on the blog listing page and in the site options there are not shown as an admin of there blog but the super admin is. This is weird seems they can still login and edit the blog.

So far i have tried:

1:I assumed this was a plugin issue so i first of all deactivated all plugins on main blog but this made no effect.

2:I then deactivated all the network plugins and this changed nothing.

3: Finally i tried this with all plugins deactivated on both the main blog and network wide and again no difference.

My Conclusion:

I may be wrong but i can only assume that some old tables have been left in the database that inteferes with this. I am not 100% but i am pretty sure it worked on a test install upto the point of installing multisite privacy from you guys.

Therefore im wondering if there is anywhere i can look for the stray settings etc.