Dear Riya,
it is important to keep in mind, that in case of radioactive isotope sources FLUKA treats the decay as a primary “event”.
Which for Co60 means, one primary “event” consists (99.88% of the time) of the two gammas plus an electron from the beta- decay.
If you are simulating photos with the two energies, you are skipping half of the decay per primary “event”. So you need to multiply the results by 2 as well to get the same as with the isotope source. Which corresponds the 1.65 factor you were seeing. (The Gaussian broadening maybe plays a role why you don’t get approximately 2.)
The third peak can be easily understand: It is the peak, when both of the gammas stop in the detector with the total energy of ~2.5 MeV.
Cheers,
David