By default, the Mobile Joomla system only creates a mobile copy of the Main Menu. Have you created an additional Menu Module for the logged in menu for mobile? If you look at your modules, you will see your main menu located in whatever position you chose (1,7, etc...) and a mobile menu located at mj_all_header. If you open the properties for the mobile menu you should see it assigned to the Main Menu via the dropdown box for Menu Name.
Create a New Module, select Mobile Menu from the module type, assign it to mj_all_header, set the proper access level, and then in the Menu Name list on the right, select the menu name for your logged in menu you want to display.
Hope this helps you.