A similar question exists for 11.04, but the answers were "wait for 11.10; it'll work there." 11.10 has arrived, and it dun broke on me. :-(
When I first started using Gnome Shell, the Gnome 3 notifications worked fine. After suspending and resuming, it appears to have reverted to the Unity notify-osd bubbles. This is annoying, because a bunch of notify-osd bubbles become little windows in the middle of the screen when the computer suspends. They also become queued up in the Gnome Shell notification bar at the bottom of the screen, all with the label "notify-osd".
If I log out and back in, notify-osd is gone and the Gnome 3 indicators are back until I put the machine to sleep. But how can I keep them permanently?