Glad my comment helped a bit. The Canon designers, in their ultimate wisdom, have dictated that AF assist cannot be used in AI Servo mode. Unfortunately, this is my favourite mode and it always takes me a few seconds to figure out what's wrong.
Sorry, I can't help with the C.fn and green light. Does the flash go off and do the exposures seem ok? If the flash is working properly, I wouldn't be too concerned about the C.fn thing. I'd just assume the function relates to something your flash can't do. Your flash probably lacks the ability to communicate with the camera. But I'd still expect a green light to come on. This should just be an indicator that the flash is ready to go and would be independent of camera settings. Are you using fresh batteries?
With the AF assist, I've found a big difference in effectiveness between various flashes. If it is working consistently on objects less than two to three meters away, I'd say it is probably working ok. They generally don't have a long effective range. Do you have more than one lens? If so, try different lenses and see if they work better. I assume you're doing all of this in the dark? I'm just guessing at this, but its possible some zoom lenses might not letting enough light into the camera for it to work very effectively. Your centre focus point is probably the best one to use, so make sure you're testing on this one.
If AF assist is a big thing for you, I've been eyeing the Yongnuo ST-E2 recently. I've heard it has the best AF Assist distance. (But its not a flash - just an infra-red flash trigger which may or may not work with your flash).
