The only thing I don't understand about that is that the carpenters that framed up the house would have used the floor plan for all dimensions. I'm assuming that they built the walls of the pantry and not the cabinet maker.
So technically all the walls should have been built in the correct position as per the correct floor plans and the cabinet maker would have built to those.
Unless the walls to the pantry are part of the cabinetry, then I can see how a difference in the floor plan and cabinet detail would have caught them out.
What ever the case, I'd be 100% sure a conversation was had about the difference in the two sets of plans.
If I was the cabinet maker I would of been asking the builder why there was a difference. If I was the builder, I would of been asking the architect why the difference.
I'm starting to think that the Architect has made a mistake and then has likely made a decision on the fly that is now coming back to bite them on the bum.