In a Custom Layout, there are no specific settings for Landscape and Portrait. It is one set of settings, so when switching you loose half of the controls.
I just was testing this and it seems that the desing-mode does it wrong. So when I am in portrait, going into the design, going back, then to landscape and then into design, it works as expected.
If I am in design and then switch orientation it goes wrong. So luckily there is a work-around, but the problem is still there....