hi, did you get an update from this. Mine seems to have the same problem. Drove home with my new second hand s-max (2.0 tdci titanium automatic gear, 2010) and on arrival (party killer), at idle, it had this faint knocking noise. Didn't have it at any other time during the 140km drive. Didn't have it when I drove it today. Like you mentionned you hear it mainly from the inside. Not sure if it followed the revs with us. It was gone on its own some time after we turned of the A/C and/or the motor ventilator stopped, so not sure which of the two would have contributed to it stopping.
No we still haven't identified it and it still occasionally happens. The local Ford dealer has supposedly had a good look around but as it hasn't happened in their presence they can't diagnose it. It still only occurs very occasionally.
The last time it happened I lifted the bonnet to see if I could better identify the area and whilst doing so I noticed the radiator cooling fan, which was running, turned off. I went back inside the car and the knocking had stopped. I did tell the garage that I thought the two could be connected but again they were unable to find anything.
Please do let me know if you find it.