I had this problem. A 2007 2.0 tdci focus. Was working fine, and parked up for a week at work, Came back to it and would not start. The immobiliser light flashing away. It then flashed code 1.1. Plugged a Delphi unit in to read and it was showing that the key was not matched.
After a quick search found this answer on another site which'd worked for my car.
Place key in the ignition and switch to position 2 on and off, 4 times within 5 seconds. You will here a bleep. Take key out and press the unlock button on the remote, and then place the key back into the ignition but leave in position 0. (off)
Leave for about 30 minutes and t will learn the transponder code. Mine fire up straight away.
the comments on the site would suggest this is a common fault near supermarkets
Hoe this helps someone