OK, I have some more information on this. Let's assume I start with an empty Inbox:
(1) When I receive a new message, I get the notification as expected. Screenshot at: http://state.tc/imgs/tb-libnotify-0min.png.
(2) After waiting for 1+ minutes, without receiving any new messages and without checking my Inbox, if I look at the indicator menu again, it shows two separate entries for the same Inbox, each indicating one new message, but with different elapsed times. At this time, there is only one new message in my Inbox, but there are two notifications. Screenshot at: http://state.tc/imgs/tb-libnotify-1min.png.
(3) After sending another test message, and still without checking my Inbox, things seem to behave as expected. Now I have two messages waiting, and the indicator shows two messages. Screenshot at: http://state.tc/imgs/tb-libnotify-2msgs.png.
The other odd thing is, after two or more messages are present, the indicator always shows "0 min" even if more time has elapsed since the message arrived.
I hope this is helpful. Please let me know if there is anything else I can do to help troubleshoot.