The FMS should modify still air MRC according to the cruise wind and cost index entered. If the cost index is zero then MRC will be faster in a headwind and slower in a tailwind to give you the lowest fuel consumption in terms of kgs burnt for each ground nautical mile.
In the 'big picture' the cost of fuel burnt is not the only thing to be considered. The cost index, calculated by the operator, feeds a second input into the speed calculation to allow for leasing costs, maintenance costs, getting an extra sector in to the day etc. Thus a correctly calculated cost index of 50 will have you flying faster than MRC for the wind, and therefore burning more fuel, but the increased fuel costs will be more than offset by the savings related to airborne time.
The lack of visible fuel savings below a certain point on the B777 might be a result of a very flat drag curve so, yes, it might be your wing.