Your keycode memory has reset itself, it's a common problem after battery discharge or short circuit. If you dig out your manual you will find a 4 digit security code on a seperate card and instructions on how to perform the "Emergency starting procedure". It's a pretty tedious procedure (I know from experience) but it'll get the car going.
Take the master key (the square shaped dark red one) down to your local Alfa dealer with the car and they can reprogram the system for you, shouldn't take them more than 15 minutes to sort it out...
Try looking in your owners manual, it should say something about this.
I think you should enter the code manually using the gas pedal. The code is the one on the code card supplied with your car.
Hope this helps