Sorry for the late reply.
Can you please provide details regarding the normalization you applied to get from the FLUKA results to your plot with ‘Response’ in the Y axis. Also, did you apply the same broadening in MCNP and FLUKA?
Looking at the results, it seems that the Gaussian broadening that you are applying in FLUKA is somewhat different to that one used in MCNP. For example, take a look to the highest energy peak, experiment and MCNP results feature a broader peak than your FLUKA result. A different broadening could be the reason behind the differences in relative heights between peaks, but still we need to take a look to your normalization to test if this is the only factor at play.