Yes, I can see your issue. I tried it and saw the same problem. It doesn't seem to be affected by pool size, air group experience, air leader aggressiveness, or HQ target. B-29s (heavy bombers in general?) appear to be very sensitive to target designation when they're in range major oil or factories. They just don't seem to want to go for anything else, and if their base is assigned to another target, say Iwo Jima, they do seem to refuse to fly (perhaps LeMay is pissed off at your target choice ). It's oil and factories they crave. (As a test, I put some oil on Iwo, and then the B-29s happily attacked the base.) If you move the B-29s to a base where they can't reach Japan (like Eniwetok), but can reach Iwo, then they do appear to go after Iwo when you select it as the target for the base. You could do the same for Leyte from some place like Manokwari.
I can understand your frustration. If you want to plaster Iwo Jima with 150 B-29s on Saipan, then by God, you should be able to! Sometimes the AI just decides it sees a more important target than what you want to go after. B-29s are happiest when they're free to go after major oil or factory targets.