There are so many things that could be causing this.

Are all those top surfaces cut by the same tool in the same set up? I can't see how you're cutting 1.7mm too deep from the side wall to the pocket surface, but then the pocket surface is only 1mm deeper than it should be compared to the bottom surface so I think this is a set up error. If you're sure you're setting your Z height accurately, its probably an error in the heights or stock to leave.