Well, I'm having the same problem with a brand new FM3, here: FW 3.02, I turn it on and once it has booted, the footswitches show "---", no lights and totally unresponsive. Everything else seems to work, even using FM Edit works fine.
More: the footswitches seem to be mechanically ok, since I manually entered setup -> FC Controllers/Onboard switches and set each switch to a different preset. It's like the factory layout was not loaded. How do I do that without doing it manually?