You're splitting hairs over concern on the one day you have the longer run. It's more what you do over time, than any particular day. Find a target and stick with it. Then, the equations don't matter - they are likely to be high or low depending on the individual. Instead, gauge your success.
Obviously if you consume those calories and don't drop weight after a few weeks, you are overestimating calories burned and need to either burn more calories and/or restrict your caloric intake. If you are on target, great, if you lose faster than expected then up them.
The equations are just guidelines and starting points, they are not set in stone. If you notice, they compute based on your age, height, weight, gender, etc. However studies have shown that if you get a room full of 100 people who have the same age, height, weight, gender, general activity level, etc, their metabolism can still vary in either direction by as much as 500 calories. That's significant and means you need to keep diligent records and adjust based on your actual success and progress.
That's why I shy from FitDay (yes, it is great that is free) and go more for software like DietPower that does this automatically (i.e. it doesn't attempt to guess based on an equation, but after analyzing my activity, food, and actual weight change, gives a very realistic interpretation of what my real metabolism is).
Here's an example of my past several days:
http://jeremylikness.goldensummitinc.com/images/blog/dietpower20060114.gif[/URL" target="_blank">
As you can see, the blue line is my goal, the red is my actual weight - it definitely does a good job of keeping me on target.
Jeremy