I had a similar thing happen copying and pasting surfaces from one C3D drawing to another. All the elevations came out scaled 1/12 in the target drawing. X,Y was all correct, but Z was blown. (Both drawings had units set to decimal feet)
I went to the User Preferences tab in Options, and in the deafult Drag&Drop Scale settings I set source and target both to feet, and the next copy/paste worked right.
It could be another facet of the same behavior (bug?), so give it a try and let us know.