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In PVsyst, the evaluation of the "Losses" of a PV array (as for the definition of the normalized performance ratio), takes as starting point the energy which would be produced if the system worked always at STC conditions (1000 W/m², 25°C, AM1.5).

The loss due to operating temperature (instead of 25°C STC) is well-known and referenced by everybody.

It is strange that nobody tells anything about the loss due to the irradiance level, which is of the same kind. Please have a look on the graphs of the behavior of a crystalline PV module (in the PV module dialog, choose "Graphs" / "Efficiency vs Irradiance"), you will see that the efficiency decreases for lower irradiances: this leads to the "Irradiance loss" (with respect to 1000 W/m²).  Therefore this Irradiance loss is a consequence of the intrinsic behavior of the PV modules, described by the "one-diode" model.

In the one-diode model, the efficiency at low levels depends on two parameters:

- The Rshunt exponential behavior: when the irradiance diminishes, the Rshunt increases exponentially (and therefore the corresponding loss diminishes).

The lower Rshunt  at STC, the more losses to be retrieved by this process, and therefore the higher "low irradiance" efficiency.

- The Rserie resistance goes with the square of the current, therefore increasing with power. If the Rserie is high (bad), the losses are higher at STC (or reciprocally the efficiency will be enhanced at low irradiance levels).

Therefore "bad" modules  (low Rshunt, high Rserie) have the best performances under low irradiance conditions (with respect to STC specification).

This may be easily understood by an opposite point of view: when you start from performances at low irradiance of a given module (say, 200 W/m2), the efficiency at higher irradiances is penalized by these losses, resulting in bad STC conditions. But in reality you buy the STC value...  

This explains (along with the temperature coefficient) why amorphous modules show a better productivity [kWh/kWp] than crystalline ones in middle Europe climates.