I have a temporary workaround for this.
Open G Hub, switch to the Guild Wars 2 profile with your settings, and next to the "Assignments" heading, click the little lock so that it's in its locked state. That will temporarily set G Hub to always use those settings, regardless of which window is open. This does mean that your GW2 binds will be in place for everything until you unlock it, so it might be annoying if you use the mouse buttons for browser or other stuff in the background. Remember to unlock it when you need it to work with other apps.
