i suffered with the same noise and a technician at ford said it was normal. it was something to do with the car resettings itself it is situated inside the engine compartment at the right hand side at the back off the engine. it is a metal square box shape thing.
I HAVE A GALAXY ZETEC 2001 WITH THE BASIC TEMPERATURE AIR CONTROLS. DOES ANYONE KNOW IF OR HAS CHANGED IT TO TO THE DIGITAL CONTROLLED ONE YOU FIND IN THE GHIA MODELS.