I'm having the same exact problem, and I've had the car to Ford time after time. Ford has done the wiring harness recall, and replaced the fan motor, and temp sensor. It still doesn't work right. I'm convinced the low speed relay is not coming on at all, and only when the temp gets really hot, the high speed relay kicks on for just a few seconds.
If I recall correctly, the Zetec low speed fan should kick in at 100 C, and should run until the temp drops to 93 C. If the low speed fan doesn't do the job, or if the low speed relay never kicks in, the high speed relay should kick in at 103 C, and kick out when the temp drops to 100 C. Don't quote me on these figures, I'm going from memory on this.
From what I can determine, the a/c fan is dependent upon the a/c pressure, and when the pressure reaches a certain value, the fan should kick on and stay on. My contour does that, no problem; however, my mystique does exactly like yours, and stays on for about 3 seconds, and then cuts out for about 12 seconds.
I still don't know what's going on, and my Ford dealer doesn't either. They started out replacing the resistor in the wiring harness, but when the resistor kept overheating, they simply removed the resistor. We're still arguing about that too.
Don't know that this helps, but we're in the same boat.
