This is the expected behaviour for v1-UI viewers.
The notice hiding feature was added in the Cool VL Viewer (it doesn't exist in the other v1-UI viewers) as a way to
temporarily hide the notices so to get access to whatever floater is below them, and until you can deal with the said notices
before logging out.
v2/3 viewers completely changed the way notices (and tips, IMs, script dialogs, inventory offers, invites, etc) are dealt with, thus the different behaviour. It would be possible to add a save and restore unread notices feature in the Cool VL Viewer, but it would be a very low priority task on my "To Do" list, so if I were you I won't hold my breath on it...
Note that you still can read past group notices from the groups themselves and can therefore find there a notice you skipped inadvertently (just open the corresponding Group Information floater and browse its Notices tab).
I might however add a warning/confirmation dialog for when you log out with still unacknowledged notices.