In WordPress version 3.1.2, if you are running a network (multisite) the behavior for users with no blog has changed. Before, users were allocated to a dashboard blog that had no front side if you chose to use one. If not, users were added to the main site.
In 3.1.2 this is no longer. users with no blog or site have a user dashboard with no attached blog or site – not even the main site. they will not be listed as users on the main site, but they will still be listed as users in the network and have their pseudo-subscriber access. (This basically means when they are logged in, they are logged in to all sites in the network but do not have admin area access to all blogs. they can just comment if “must be logged in to comment” is checked on any blog/site.)
If you still need users added to the main site/blog (for example in cases where you have a forum synced up with the main site for support) then you will need to add users to the main site when they sign up.
This plugins may help: Multisite user management.
Note: this behavior does not affect BuddyPress profiles.