I had a 12.5k service on my 2l TDCi Focus in Nov 06 and experienced a similar problem, took it straight back to the dealers and they had left a vacuum pipe disconnected - worth a check, Had the EGR done about May 06 with no problems.
I collected a 2.0TDCi just over a week ago. Had to wait about 3-weeks for it to be shipped (from Germany I think) to the dealer. It's a recent build as one of the plastic parts I looked at had a date stamp of 01/06. My car has plastic strips along the sills, submarine lighting and an aux socket already installed in the glove box.