Mike Sandford and Justin Kuo came up with the correct answer. Good job. After I did my pre-cal I put my bike on my rack and drove 40 miles to the race course. During that ride the front wheel started spinning backward. After I finished the course measurement I again put my bike on my rack and drove 40 miles to my home to do my post cal. And again, the front wheel of my bike was spinning backwards during this drive. That's how the starting count of my course measurement and post cal ended being smaller than the finish count of my previous measurements.
As far as I know this hasn't happened to me before, but it's possible that it has and I just didn't notice. Especially if the wheel was spinning forward there's a good chance I wouldn't have noticed the count numbers being odd. Has it happened to anyone else?