I am using a custom signup page in my theme folder. When

I am using a custom signup page in my theme folder.

When a user signs up, they become a user in the Network, but not in the main site. Meaning I can see the user in Network > Users but not in the user list of the actual site itself, so they can't get access to any content.

Have looked at pro-sites, networking settings and a half dozen other places... is there some checkbox hidden somewhere that enables this?