A few things to consider:
1. A very fit runner running a marathon would burn about 3000 calories. That is one pound...and that 3000 calories could easily be mostly wiped out in one meal at a Pizza buffet.
2. I saw a documentary that took a bunch of couch potatos from sedentary to a marathon in 9 months. One of the ladies finished the marathon, but remained about the same 30-40lbs overweight that she was when she started. Steady, increased training up to a very high amount for almost a year did not cause weight loss, only fitness ability. She didn't eat for weight loss, so it didn't happen.
3. Frelee and durian rider probably ride 50+ miles A DAY, 5-6 TIMES A WEEK. That said, it's about the food. If you are taking in the same amount of high carbs on rest days as workout days.. there is no where for that energy to go, so it gets stored. They can eat tons of carbs cuz they work out tons. One thing to try would be high protein/healthy fats on rest days, higher carb leading up to a workout.
4. If you really feel that you are eating healthy, tier is one change you can make to your riding that will likely see immediate, positive results: INTERVALS. Scientific research, and my experience tells me this is true:
Over the winter, due to weather and busy-Ness, I didn't ride much, often I would ride in my indoor trainer for only 20 minutes, twice a week...but I would do an intense interval session of Max sprints followed by short recoveries...bu doing this and "generally trying to eat whole foods" ( no calorie counting for me). I lost fat, and became a faster, stronger rider...