Hello-
I tested this on an upgraded site, and to be sure I then made a fresh install and tested with that. The result is the same on both sites... having Mobile Joomla 1.0RC installed breaks the ability for logged-in users to see protected content. 
To replicate: 
   - install fresh copy of Joomla 1.7.
    - add a user, put him in "registered" group.
    - go to a menu item, and edit it to require the "registered" group.
    - Test. To public, menu item is hidden. Log in as registered user, and menu item shows. (as expected)
    - Install Mobile.
    - Repeat above test. You will see that logging in as "registered" user does not cause the menu item to appear.
  
I hope this can be resolved. I LOVE the functionality and design of this plugin (particularly the WURFL integration) and I want to be able to use it on my upcoming site. Thanks for your attention.