Users not being assigned to main site upon registration

Since the 3.6.1 update, anytime a user registers with my WPNetwork, they are not being assigned to a site, whether it be the site they were browsing when then clicked Register, or the main site for the network. When I check the users in the Network Admin section, it shows them as not being associated to any site at all.

I have been through all the menu and am able to manually apply user to a specific site through both the Network Admin and a specific Site Admin, but see no settings for them to be automatically added. Is there a setting I am missing? Have you heard of this issue before?