Our subscription site and the membership plugin

We've been working with wpmu for a while now use many of your plugins and have had success with membership premium since 3.4.5 Since the new release 3.5.6 there has been some sort of conflict on the site could be the theme could be another plugin- It's hard to say though I have recently deactivated all the plugins excluding membership and it still didn't work, so my guess is that it's a theme issue.

In a little less then a month we are doing a major overhaul and planning on dividing our site into two different pages and that means it's going to be a good time to make some changes without dragging out the changes over a week or two for our users.

Our site has many plugins and considerably heavy on our server. we have 800 new users since March and expect over 2000 by the end of the year.

Some of the Major plugins that we're using are: Membership, bbpress, buddy press, communities, forums, custom login by Austin Passy, Usquare by br0, bookshelf slider by Sergio Valle, Our Active Theme is Organic Natural Theme version 2.2.3 by Organic Themes. We spent some money on it so we're not excited to get rid of it but would consider something simular to it. (it needs to be reactive and simple, clean with lots of options.)

I'm looking for suggestions in moving forward and being able to update our membership plugin, and would like to hear suggestions about what we can do in moving forward.