Dear Ryan,
In SSC Versions 41 (SAM 2015.1.30) and earlier, for the pvsamv1 compute module, annual_ac_net is the total annual output of the inverter in kWh after any AC wiring and transformer losses, and annual_energy is the total output of the system in kWh. The two values are equivalent unless you specify non-zero values for the adjust input, which is designed to account for operating losses such as those due to system outages for maintenance or forced by the grid. (The difference between annual_ac_net and annual_ac_gross is determined by the acwiring_loss and transfomer_loss inputs.)
In later versions of SSC, to avoid confusion, we removed the annual_ac_net output so that pvsamv1 only reports annual_ac_gross and annual_energy. The difference between the two is determined by acwiring_loss, transformer_loss, and adjust.
Best regards,
Paul.