Analysis of homoepitaxial growth on Ir(111) by scanning tunneling microscopy (STM) reveals that two different phases nucleate. We find islands in the regular face-centered cubic (fcc) stacking as well as in the hexagonal close-packed (hcp) stacking. Performing STM measurements on fcc and hcp areas shows an apparent, voltage dependent height difference of up to 6% of the regular layer distance. By applying first-principles calculations, the voltage dependent height difference can be attributed to the difference in the electronic structures of the two phases. The atoms in hcp stacking appear lower for a wide range of tunneling voltages, opposite to the actual relaxation.