Well, what I meant would have been that the software is smart enough to see that there are two playlists made up by seamless branching. Since it can’t do AVCHD seamless branching (in this scenerio I’ve made up), it instead encodes the film twice as two separate streams, doubling the streams visible to you for the BD5 and BD9 but not the proper blu-ray sizes.
Like I said, it’s a stretch. But it’s a weird thing you’ve noticed and I can’t come up with a better explanation.