I had this problem with Membership Lite, I just upgraded to 2.0 and it is still there.
I get a note from Paypal that I have a new subscription, I have to manually change the person's status on WP (couldn't figure out why, but that's an irritation, not a bug). It worked fine before, but lately I am unable to change someone's subscription level. I can update their Membership level, but I can't designate which is Monthly and which is Yearly. That spot is blank, and when I go to change it, I go through the proper motions, but nothing ever changes.
(BTW- I did deactivate all other plugins and the problem is still there)