Hi all
I find the problem different than as suggested that being a theme issue.
I have a membership site that contains just the use of s2member level 1 for all members and of cause there is the non-member view and also the admin view of the site.
Now I initially built the site using the Thesis theme 1.85 and wordpress 3.4.2 and it all worked perfectly. That is when a non-member visited the site they could only see the menu links to pages and posts that had no s2member level (a normal visitors view).
When a member was login he could see the menu links to all pages and posts that had s2member level 1 and what the normal visitor would see.
Because the site was designed for a client I had a menu link called admin which contained a few sub-menus as well which I designated these pages at s2member level 2, when logged in as admin he could can see all the menu links but the members and non-members could not see the admin menu links.
This all happened without any additional coding etc.
As soon as I updated to wordpress 3.5 the menu links that remained hidden according to access level were now appearing to anyone who visited the site only restricted by s2member’s ‘Membership Option Page’ redirect.
I have not found a solution yet as I have only found this post by using this forum looking for reasons or others who have had a similar problem.
So from my experience it seems to be wordpress newest version of 3.5 that has somehow changed the menu structure and how it works with s2member restrictions.
I also have tried it with the newer version of Thesis 2 and am having the same problem so the most common denominator given my experience is going from WP 3.4.2 to WP 3.5