Take a look at the documentation for Keymaps:
@olmokramer, @Alchiadus: After reading the above documentation and your comments it seems, the keybinding works exactly in reverse, what would be desirable, and in the current state it is not possible at all to define global keybindings.
(The first, most specific dom element consumes the key combo, and there is no global decider who may override/protect some global keybindings)
It suffers the exact same issue what normal firefox/chrome suffers. Ie. having a flash application in focus on the current page makes
It is the same with atom. Having a widget in focus on the current page may result some “global” keybindings to stop working. The most prominent is Ctrl-PgUp and PgDown.
A workaround would be to define the exact same keybindings to each panel (file search, directory tree and main editor), but it is designed to be broken in future simply because it does not take into account there is a need for global keybindings.