Landed vessels are loaded a few meters off the ground and dropped on the surface.
I've noticed for a few months now on both patches 1.5 and 1.6 that sometimes when I load crafts on the surface of Duna or Eve they will spawn above the surface instead. It's happened several times to landed bases, rovers and EVA kerbals.
I'm playing on a save that dates back to 1.4.5 but I'm not having any other issues with it. Unfortunately it's filesize is too large to upload as I've completed loads of contracts with it. Let me know if there's something I can do to get it to you anyway.