Hm, it's been quite a while since I've touched Orbiter but I recall having issues landing the DGIV on the Moon. The craft would call out altitudes several kilometres above the surface and "crash" when it reached what the ship thought was 0m above the surface (despite actually being several kilometres above the ground). Not sure if I'm remembering everything correctly.
I think it was linked to the addition of elevation maps, but perhaps it was all just an issue on my end.