I ran into this problem recently, and found this helpful post regarding how to fix it:

http://auroral.co.uk/2011/03/29/changing-your-wordpress-multisite-admin-username-network-admin/

Update: Apparently that post no longer exists. I’ll see if I can find another one to replace it. I honestly don’t remember what exactly the old post had that I found so useful, but hopefully I can find another one that is also useful. 🙂

Update 2: Here’s the new one:

http://tahirtaous.blogspot.com/2012/09/how-to-change-wordpress-multisite-admin.html