Finder vs. shell

I am trying to move a large number of files (600,000 or so) from an AD-connected Windows Server to an AD-connected XServe. When I copy the files in the Finder, I get all of the Windows-AD-related groups and permission (as I had hoped). I DO NOT get these when I copy the files using the Windows computer, only while using the Mac. What I want to know is, is there a CLI application to do the same thing? I don't want to have to rely on the GUI. Any ideas? Thanks.