First of all, you can't and you shouldn't set the initial spin separate in the electrode and the electrode copies.
The electrode copies are the first and last NL and NR atoms in the central region, where NL and NR are the number of atoms in the Left and Right electrodes, respectively. These atoms in the central region must be exact copies of the electrode atoms, by position (relative the edge of the cell), element, and order. This is a fundamental requirement in ATK 10.x and higher, and is related to how the boundary conditions as well as initial matrix elements are set up. This is also why it's not necessary to set the initial spin of the electrode atoms, you just set them on the electrode copy atoms, and the setting is then automatically copied over to the electrode.