I made a similar run, setting the electron and photon energy grids to your values (Ekin_min=1e1, Ekin_max=1e8; E_gamma_min=1e4, E_gamma_max=1e8; long_min=0; long_max=360; lat_min=-5; lat_max=+5). I did not use anisotropic IC, just to save time. Results:
1) for E_gamma_factor=1.5 (like in your run) I get the same jagged spectrum of IC.
2) for E_gamma_factor=1.3 (just to make it smaller), IC came out with a smooth spectrum.
3) for E_gamma_factor=1.19 (a test), the IC spectrum is jagged again.
I think it is related to the fact that Ekin_factor=1.3 in these runs, and there must be some interpolation problem in GALPROP. Anyway, setting E_gamma_factor=Ekin_factor seems to work for now, and the other cases reveal a problem.
Please try re-running your configuration with a different Ekin_factor (the Import button in the Download Results section will copy all the parameters into a new form), and if you find the same, would you kindly file a bug report via http://galprop.stanford.edu/bugs/
? I am asking you to do this instead of doing it myself because it will set a good example if users outside the GALPROP team participate in bug reporting