Persistent memberships across Subsites - now broken

When I first set this up a month or so ago, membership levels created at the default site were also created in subsites and my permissions were persistent across all sites. Now, those subsite levels are gone and I can't find a way to maintain permissions across subsites. Is this not possible any more?

Ideally, I just want one registration process and allow people to maintain their membership permissions in each subsite. The subsites need to maintain some sort of autonomy but the membership belongs to the overall organization, not the subsite. Is this possible any more?
Thanks!
Tom