fiberdesk ignored the "add quantum noise" option during parameter variation. This bug is removed now. Below you see the variation of the input power in a fiber amplifier (1 W pump, rate equation without ASE) and the output power as a measurement result. Up to ~10 mW the amplifier gives the full small signal gain then saturuates and finally increases linearly because the output power is in the same order of magnitude as the input power.
However, if you perform the simulation again including ASE, the total output power is dominated by ASE (in the example 13 mW) in the range below some µW of seed power.