Last working version:
gnome-shell-3.2.1-2.fc16.x86_64.rpm

Description of problem:
1. Under gnome-shell-3.2.2-1.fc16.x86_64, traditional notification icons (those found in the bottom-right corner, such as the "classic" NetworkManager applet, Skype or XChat) sometimes don't appear, and the associated menus never pop-up when clicked.

2. The right-click action is intercepted and a gnome-shell bubble pops up with two actions, including "Remove". This should not be, as some traditional applets present a different menu on right-click. This menu could possibly be reserved for a long right-click (similar to the icons on the Favourites area in the Activities overview).

Other package versions:
gtk3-3.2.3-1.fc16.x86_64
mutter-3.2.1-2.fc16.x86_64
clutter-1.8.2-3.fc16.x86_64

From .xsession-errors on gnome-shell-3.2.2-1 (relevance not known):


** Message: applet now removed from the notification area
gnome-shell-calendar-server[20328]: Got HUP on stdin - exiting
org.gnome.Shell already exists on bus and --replace not specified
(gnome-shell:20319): folks-DEBUG: individual-aggregator.vala:305: Setting primary store IDs to defaults.
(gnome-shell:20319): folks-DEBUG: individual-aggregator.vala:333: Primary store IDs are 'eds' and 'system'.
    JS ERROR: !!!   WARNING: 'assignment to undeclared variable batteryMenu'
    JS ERROR: !!!   WARNING: file '/usr/share/gnome-shell/extensions/presentationmode/extension.js' line 26 exception 0 number 156
    JS ERROR: !!!   WARNING: 'assignment to undeclared variable removeTopBar'
    JS ERROR: !!!   WARNING: file '/usr/share/gnome-shell/extensions/icon-manager/extension.js' line 88 exception 0 number 156
    JS ERROR: !!!   WARNING: 'assignment to undeclared variable iconManager'
    JS ERROR: !!!   WARNING: file '/usr/share/gnome-shell/extensions/icon-manager/extension.js' line 94 exception 0 number 156
      JS LOG: GNOME Shell started at Sat Jan 21 2012 21:39:16 GMT+0000 (GMT)
** Message: applet now embedded in the notification area


No unusual messages of which I am aware from the applications that place the icons.