You are going to need to clarify most of that as it’s not really clear.
What is ‘Partially inactive’ with the menu bar[?sic] when on buddypress.org
What WP admin pages?
Explain ‘Nightmare’ it’s a big word ‘Add All Nav Links to BP Adminbar’ does not solve any problems it’s simply an enhancement to that which functions perfectly well – doesn’t it ?
Explain exactly what you think you are missing on buddypress.org
Chiming in here…
@hnla is correct (as well he should be, with all the help I got from him building the plugin). Add All Nav Links to BP-Adminbar does not modify any links inherent to the adminbar itself (My Account, My Blogs, Notifications…). It simply adds Buddypress and WordPress page links to it and allows you to customize how everything is displayed.
Im not sure why it only solves part of your problems.. But I wrote up an article complete with plugin to dynamically add all your pages to the buddypress bar.. Maybe this will help?
http://erikshosting.com/wordpress-tips-code/add-pages-to-buddypress-admin-bar-dynamicall/