Aside from this, while there are a lot of us that would love to have it, most players want to get in and out of the mission quickly. Look at the now broken/removed docking sequence for ESD. Back on release you have to take the time to fly close, open doors, and fly in. It didn't get fixed because the impatient few were…
I would say try to find your way back to the key mapping and if it has a "Restore Defaults" use that. Or try to manually remap. The problem fixing it is how many other functions are mapped to it.
I have noticed that it happens when you open mail intended for a different character. I fixed my issue by having someone mail the character I was on and opening it. Its a weird workaround but it worked... after that, try to keep a mental note of what toon mails and if you see the icon again get on that toon.
What if you finished the event, got the ship, the admiralty cards etc. but did not get the transponder? I have looked in both event reclaim and z store. Any suggestions before I submit a ticket?
I have noticed that it happens when you open mail intended for a different toon than the one you are on. If you have some one send a mail specific to the toon you are currently logged into it will remove the "waiting Icon". Not sure about chat, usually just use the Xbox voice and leave it at that.