I agree, if it were the time it takes you to cap them you'd expect the last bottles filled to have higher carbonation than the first bottles filled, since capping goes much faster than filling.
I would look at something else in your procedure - longer time settling before bottling, different yeast strain the flocculates better, different racking cane that doesn't pull up as much from the bottom, etc. You can intentionally pull some yeast off the bottom of the carboy when you rack to your bottling bucket or add some fresh yeast at bottling, and see if that helps.