This posting is older than 6 months and can contain outdated information.
Remote Buddy always automatically switches to the context menu of the
Behaviour that is currently active.
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