As Behaviours are not only chosen if the active application is 
supported, but also if one of a few apps (incl. iTunes) is running in 
the background, the iTunes ones will likely be chosen if it is 
running in the background - and thus its menu is displayed.

The fact that RB also makes background apps part of the choice is 
simple: nobody wants to switch to iTunes (or other media players 
supported that way) each and every time they work on something else 
and only want to change tracks or play/pause using the remote.

Hope that explains the "why" part of the question.

As for the option to start right at the top level of the menu: yes, 
there is. Go to Preferences > Hardware > *Your remote* and click on 
the entry for the menu button. You can now choose an alternative 
action that will always open Remote Buddy's menu in the root menu level.

You can also assign this action to another button, so that one button 
opens the main menu at the context menu level and the other one at 
the main menu level.

Best regards, 
Felix