Unfortunately I couldn't find a firm answer to your question in the forums. Here are two different answers, the first is worth a go, the second at least explains why it's happening.
"If you have a key fob to lock your doors you can do the following, insert key into ignition, turn it on to acc and off a total of 8 times quicklyyour doors will lock and unlock and reset system, but you have to push the disarm button on your key after for it to work. If no key fob, then you will need to have someone with a code scanner completely reset your ECC."
2nd answer
"There is a chip in your ignition key that transmits a code to the vehicle. If that code doesn't match a code that is stored in the computer's memory, it will not allow the vehicle to start (and cause the anti-theft light to blink rapidly while trying).
It is normal for the anti-theft light to blink slowly when the vehicle isn't running.
If the anti-theft is the reason for the no start (rapid blinking while trying to start) then try another key. If you do not have one then one will need to be programmed at a locksmith or Ford dealer that has the equipment capable of doing this. This will need to be programmed to the car, so you'll need to either have it towed or find a mobile service that can come to you. If another key won't allow it to start, then the system will need to be diagnosed, repaired, and programmed by someone who has the proper equipment and know-how (most likely a Ford dealer)."
In a nutshell, sounds like the old key information is stored in the ECC and won't recognize the new key. So give the first suggestion a try.
Good luck.