The only thing I can think of is that you might be running with an enabled fade-plugin (for compiz). That does not yet include an exception match-rule for notify-osd. Could you check that with the command:
gconftool-2 -g /apps/compiz/general/allscreens/options/active_plugins | grep -nHR --color=auto fade
If fade is actually activated on you system you'll see it being highlighted in the output of grep. If not, nothing will be outputted by that command.
The only thing I can think of is that you might be running with an enabled fade-plugin (for compiz). That does not yet include an exception match-rule for notify-osd. Could you check that with the command:
gconftool-2 -g /apps/compiz/ general/ allscreens/ options/ active_ plugins | grep -nHR --color=auto fade
If fade is actually activated on you system you'll see it being highlighted in the output of grep. If not, nothing will be outputted by that command.