There is a generic FMGC model for each aircraft type. i.e. A320, A330 etc. In order to tailor each engine type and airframe this is adjusted slightly. An A321-211 (CFM-56 5B3 with singular annular combustion chamber) may be 1% more efficient than the generic model. It will have a bias of -1. The dual annular combustion chamber version may have different bias. Add on top of this the degradation from engine and airframe wear/drag as the aircraft ages, you get the the FMGC bias. So, aircraft/type bias (contained in the FCOM) + increase in drag/fuel burn % = FMGC bias.
Google 'Getting to Grips with Performance Monitoring' from Airbus.