Hi,
Just another possibility which may be affecting your remote key controls.
When I purchased my 2005 S-Type in Oct 2006, I found that the second Key Set did not operate. I visited my dealer in Glasgow to purchase a new battery for it, thinking that was all it needed. However they advised me that a batch of Key Transmitters were in fact faulty, and they arranged for the car to be brought in the following week to have both key sets modified and reprogrammed.
This was done under warranty and they have worked fine ever since.
Can't say how many cars were affected by this problem or if it was just a UK problem, but just thought I'd mention it just in case.
Hope you get it sorted soon.
Regards,
Inver.

 

It may well be that they fitted some foam as per TSB S527 (see the stickies).
Also worth checking JTB00106 and S501-18