Ah, the variables we encounter in our endeavor to accurately measure courses!
As Mike and Pete said, the un-weighting of the front tire adds length to the uphill section. The steeper the hill, the more length is added. But, if you wobble, you are canceling that un-weighting factor to some extent. If you wobble too much, you over-compensate for the un-weighting, and the segment is shorter than what your Jones would indicate. Such a dilemma!
Unless the hills are longer than a couple-hundred meters, and so steep that you wobble excessively or walk, I don't think it should be a material difference. If you do walk, be sure to lean on the handle bars as you walk, to give some compression to the front tire.
That will be an issue I will try to address when the snow melts - the difference in clicks between uphill and downhill rides on various grades of roads. Anyone else is welcome to note their observations, so we can compare variance, and also reference tire types - hard pneumatic road tires, hybrid-bike tires, mtn. bike tires, and I will contribute data for airless tires with a 120 psi equivalent.