I had a very similar experience. Exercise pays off in general health and the way your body looks, but calorie reduction is the key to losing fat.
Something else to consider are the “health standards”. Usually these are averages of large groups of people and they make a good rule of thumb guide, but they contribute very little to an accurate prediction for individuals because they cannot take our unique biologies, environments and behaviors into account.
Your calorie deficit might fall into this category — mine did. Through trial and error I have found that I maintain my weight at around 1200 calories a day and gain or lose when I go to either side of that number. Exercise has some effect, but not much.
I’ve also found that not just what I eat, but when I eat it has a large effect. I try to go easy on carbs, and limit them to mornings or early afternoon. Carbs turn to sugars so quickly that eating them without being active is a sure fire way for me to gain weight. I tend towards protein when I know I’ll be reading, writing or sleeping afterwards. I’ve also found morning fasting to be helpful.
If you haven’t read it yet, I strongly recommend The Secret Life of Fat. It’s well written and very informative, but the best thing is how the author shares her frustrations and insights. Knowing that losing weight is a challenge even for people with PhD's in microbiology is comforting.
Congratulations on maintaining a healthy lifestyle and the insights about how your body works. It sounds like you’re on the right track, so keep up the effort. The best health insurance is a healthy lifestyle.