I have used the Adminimize (http://wordpress.org/plugins/adminimize/) plugin (To restrict access to certain menu items depending on user role) and Admin Menu Editor for a while now. Recently however they have started to conflict with each other.
Adminimize works perfectly with both plugins activated, but fails once Admin Menu Editor is used and it's new settings are saved. Previously Adminimize blocked items then appear in the menu. If Admin Menu Editor is then deactivated, Adminimize works correctly again.
As said above, they previously worked in harmony with each other.
I am using WordPress 3.6.1 and the latest version of both plugins.