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The Harris-Benedict equation developed in 1919 is used to estimate BMR is based on averages. The Harris-Benedict equation actually doesn't estimate BMR but rather RMR (resting metabolic rate) because the test subjects did not spend the night at the test facility. Also, the equation does not take into account body composition such as the percentages of muscle and fat composing your body. It is less accurate if you have a non-typical amount of muscle because muscle burns calories and fat does not. Only calorimetry methods are accurate for determinining individual BMR.

The Harris-Benedict equation is known to over estimate weight loss by about 5% and it has an error range of +/- 14% (see reference below). These errors alone could account for the difference between what you are experiencing and the estimations from the equation. By the way in the 1990's the Harris-Benedict equation was replaced with the more accurate Mifflin equation for determining RMR. Some studies suggest that both methods are only accurate when applied to groups of people and should not be used for individual estimates.

There is a fairly good review of equations for calculating BMR and RMR on this web site

Reference
The Harris Benedict equation reevaluated: resting energy requirements and the body cell mass, American Journal of Clinical Nutrition, pp 168-182, 1984

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