Hi Jesse,
The Library files preserve the worldspace location and size of the data; so what I expect is happening is that your world extents are set differently between the two files. Select the library in and go to layout view and zoom out; I bet you’ll spot an island of terrain somewhere.
Set the world extents in your second file to match that of the first and everything should be right.
Although this might seem annoying at first, its a very useful thing, as the imported terrain will have the correct horizontal and vertical aspects and can “drop in” at the same part of the world as they actually occupy, allowing you to import libraries rendered from a couple different render extents (for example, one file might have a large scale overview and another a detail region) and have them just be right. The next version also has a “force localspace” option that makes all data import in localspace for manual placement as preferred.
I think the missing feature here is a “synch project settings from” menu option that will let you import all the render extents, vertical scale, etc from a different project file. This would substantially simplify multiple-file projects. This is on the feature list; I’ll see if I can move it up.