I have the same issue....most of my apps were created with the app wizard and thus have just the login page. In NT6 apps, this was the only page used during login and log out.
Looking at the web3 example, I noticed a new logout form page. It has embedded code to log out and delete the session. So I copied this form page to my apps. It does the log out and deletes the session and no stray menu items remain when they should not. However, if I try to use this as a pop up, it does not work.
I also noticed in the web3 example, there is an option to logout with JavaScript code. So I started adding this to my NT7 apps and now my logouts behave as they did in NT6.
Thanks,
Jeff