I am not an expert on anything and have struggled with weight my entire life, that being said my heart rate monitor and my garmin both give me some wild estimate about how many calories burned during a work out. I don't believe either of them. My garmin would read I had burned more than 700 calories on a 10 mile 1 hour mountain bike ride. There was no way. "The Daily Plate" seems to give high estimates of calories burned too.
The Iphone tool sounds great but I think I would take Veronica's advice and go see a nutritionist or a doctor or both.