I not sure how obscure this issue could be, but here goes:
I've been using Membership (premium) 3.4.2 successfully for while, and let me say it took me, even as a fairly seasoned Wordpress/Buddypress developer a fairly long time, to get the Membership plugin to play-nice with a clients Wordpress-multisite 3.5.1 + Buddypress 1.6.4 + bbPress 2.2.4 framework. Still, our site + WPMU Membership 3.4.2 works amazingly well. I only upgraded to 18.104.22.168 (today) as I wanted to reduce the membership upgrade period down to "0" days, which 22.214.171.124 now allows. At this time, the only 'payment gateway' we're using is the 'free subscriptions gateway'. Our issue (luckily I've only activated 126.96.36.199 on a mirrored test site) is that since upgrading to 188.8.131.52, when a new user signs-up for a subscription, they show up in the 'all members' area of the membership plugin, BUT they not longer have a subscription + membership_level assigned to them, nor is there any gateway listed. Users do also show up in the Wordpress 'all users' area, but those same new users DO NOT show in the Membership Dashboard. If I put the Membership 3.4.2 files back in (via ftp) then everything works 100% as it did before (i.e a user signs up, selects a subscription, and is assigned a subscription, membership level & has a gateway listed for their username). It boggle my mind as to what the issue could be with our setup + the 184.108.40.206 version of the Membership plugin. I've tried this repeatedly on 220.127.116.11 and new users keep piling up, but no subscriptions and being assigned to theme. Like I've mentioned, reverting back to 3.4.2 and everything 'just works' again. Kinda odd. It's rare that I can't work through these types of issues, so I'm 'hoping' that someone here has what could easily be the very obvious solution.
Otherwise, the Membership plugin is very impressive, not perfect, but very impressive.