Dear Zeenat,
You probably accidentally ticked the errors box in the plot settings (see picture below). This will plot the statistical uncertainty of the bins and not their value.
For normalization, you don’t have to put anything. In that case, you will get the results in the FLUKA defaults (per primary most of cases). You can put the real intensity/activity of the source, to get values comparable to reality. However, it doesn’t make any sense to use the number of primaries as normalization, since that doesn’t have any physical meaning.
Cheers,
David