The unit cell you probably defined with `kwant.lattice`. The modes of the leads correspond to a folded Brillouin zone in the direction of the translational symmetry that the leads have.
If you use a direction that needs more than one unitcell length, say ``` lead = kwant.Builder(kwant.TranslationalSymmetry(lat.vec((2, 0)))) ```, then the Brillouin zone will be folded `2` times.
Besides that, the direction can influence the degeneracy of the levels. For example, in a honeycomb lattice, a lead with zigzag edges has non-degenerate bands, and one with armchair edges has degenerate bands. Again, this is because of how you cut and fold the Brillouin zone.