I would first go back and check that all your stats were loaded in right when you put them into FitDay. It may be calculating for you based on erroneous information.
Also, while I agree that 204 seems extremely low, I think that 696 seems extremely high, but I guess it depends on how big you are and your fitness level. Yesterday I did the exact same thing as you...45 minutes at 5 mph (a 12 min mile) and according to my heart rate monitor, my calorie burn was 309 (though as a small 5'2" person at 42 years old, I don't burn as much as some others would to begin with).
Other than that, my suggestion is to just monkey around with what you put into the activity log...if you are sure about your burn, put in a faster pace or another activity that gives it to you in about the same amount of time.
It's definitely one of the shortcomings of FitDay, and the moderators have been HUGELY nonresponsive to adding a custom exercise option as we have with food. As a matter of fact, they've been hugely nonresponsive with respect to just about everything.
And now that you don't have to be perfect, you can be good.