Comment 10 for bug 568401

I've just found why I'm having this problem with plain local login (not with VNC). I had my Windows key mapped to Hyper, I changed this to default behavior (Super key), this fixed it for me.
I have downloaded the indicator's sources and I can see in indicator-applet-0.3.6/src/applet-main.c that the shortcut passed to tomboy_keybinder_bind() function is either "<Super>S" or "<Super>M"; so the "<Super>" part did not work for my system.