That's not a problem of the scenery, but something that sometimes happens when you go to a scenery with a different ground altitude than the one you started with, it can happen everywhere, even with default sceneries, depending where you start and where you go.
The usual fix, is to go into Slew mode, and press one of the arrow key, just enough to move a tiny bit, which will be enough for the correct altitude to settle in, then exit Slew mode.
