Hmm... I've been wondering about those erroneous Notification Numbers that sometimes appeared, sometimes creeped up.
I remember in Beta one could Navigate the most left Icons and there were two of them. Classic Local/Direct chat and the new 'System chat'. That toggle is gone for all I know and seems locked to System chat.
Are we missing an entire chat channel now where Messages get buried unread?
No, there are three possible tabs (Local, System, and Wing)
Maybe more, I'm not sure.
But local chat, i.e. your main player to player chat, can get really bogged down with all of the online/offline, sysauth, and whatever other messages. You can clean it up considerably by turning off notifications.
As for messages getting lost, friends and I have been experiencing problems receiving messages from each other. Someone will initiate, but then no further correspondence is received either way.