Ah, so you create the second uv set all in UDK? Yeah, it was sort of on a whim; I just search about how to create lightmap uvs in Maya to bring into UDK. Since the tutorial specified to use the uv set editor to create the second uv set instead of the 'create new uv set' toolbox, I gave that a try and that worked. :)
Just figured I would update this thread saying how I fixed it: I had to use the uv set editor to create a new uv set, the problem seemed to be with the create new uv set toolbox.