We've discovered today that custom channels like 'The Legendary' become unavailable to send to or receive messages from while you are in a Mission instance or the SG base. So keep that in mind when playing for the time being. You may miss chat while running missions.
Yeah its surprisingly annoying, it'll be annoying to pass information in game quickly about forming tf's or teams as whoever is doing inviing will need to PM people directly if they ain't sure a person is in a mission or not. I've been forced to refer to my Global friend list to track who is in mission and who is not so I know who will be able to get messages through The LEgendary chat.
Global Friending is a must. This is kinda why i ship everyone in the custom channel a friend invite
The chat issues have seemed to resolved themselves sometime later, everything is all green again.