In some cases, for example Bidirectional systems, the simulation is run multiple times for a section of the layout to converge to an answer. The signal index then corresponds to the signal that will be displayed. Generally the simulation will converge as more iterations are used and the desired signal will have the largest index.
Not exactly the average, but for example in a bidirectional simulation OptiSystem will first run the calculation normally, but if there is a loop or if the project is in a situation where the input signal is fed back to through a component, it will run the simulation again keeping track of the original signal as it propagates through the system.
I think a better example is to just look at the “Nonlinear Optical Loop Mirror” sample file from the “All optical processing” samples folder. Part of the incident signal that is passed through the coupler takes a bit longer simulation time to reach the nonlinear fiber, to correctly model this the simulation is run again while keeping track of the original signal still propagating. Thus, at the Optical Power Meter you should view the signal at index 1.
Hope this clears it up, but let me know if it is still confusing for you!