I'm not really sure how to describe this, but my car has been doing this since day one. I don't know if this plays into it at all but I have a manual transmission. Sometimes (not every time) I start the car and let it idle, about 10-30 seconds after the vehicle is started it makes a thunk noise. It is not extremely loud, but it is noticeable. It almost sounds like something is engaging. If my foot is on the brake pedal or the floorboard I can actually feel a small 'bump' at the same time I hear this noise. I asked the Ford dealership what it was and they told me that it was the A/C compressor engaging. They said that even if you don't turn it on it will come on every so often so the compressor doesn't freeze up. I am not 100% convinced that this is the problem. Has anyone else encountered this or know what it is?