Mark,
You are right about a measurement all on the same day. I have found that with measurements you do on different days there is more apparent consistency when you figure the distance based on average constants.
If I'm working over a long period of time I always try to do intermediate calibrations. It happens fairly often that the effective constant varies more than 0.08%, and there's always the chance that this will catch you with an excessive difference between measurements.
Interesting about the different tires. Another difference between those tires is the relative thickness of the layer of rubber. I'm thinking that is important as well-- and may relate to the problems folks have had in using small-diameter wheels as in fold-up bikes.