I did flatten the lot but yes, I've run into that before. I think the problem is that it's not a full 2 storey and the windows are programmed to fit at exact levels. The gable on the right isn't high enough to reach that level. I'm pretty sure that the gable would tie into the hip roof and it only looks higher because of the perspective.
And later...
Boy, I'm like a dog with a bone. Once I get my teeth into something, I can't let go. I've just spent an hour looking at photos of Victorian bungalows to see if I could find an example of what I'm talking about. Anyway, if you change the perspective of the photo, you would see that the side of the gable is flush with the side of the hip.
I'm pretty sure it's a programming issue. I might end up making it a 2 storey but now I need breakfast.