Thin films of MnSi(111) in B20 structure formed by reactive epitaxy on Si(111) are studied using scanning tunneling microscopy (STM) and density functional theory calculations. Coexisting root 3 x root 3 structures with high or low corrugation are observed and assigned to different Mn coverage by using a detailed analysis of simulated STM images. Comparison with our interpretation of STM images of films previously grown by codeposition of Mn and Si provides us with evidence that the stacking sequence of Mn and Si lattice planes depends on the growth protocol.