I had a similar problem to this ages ago with my 97 Fiesta. The cause of mine was water leaking into the passenger footwell (a common fault on Fiestas) and the water then got into the ECU which is located under the carpet in the footwell.
This buggered up the electronics and caused the immobiliser to play up.
Once it dried out, things worked fine again.... unti the next rain storm which permanantly knackered the ECU.
Was very expensive to repair so might be worth checking for leaks before it gets to that stage.
ColH
August 2008