Are you using authorised weights for baggage as opposed to actual weights?
The discrepancy was probably due to the aircraft GW being higher than as per the loadsheet and hence the FMGS through INIT B.
The speeds on the PFD are calculated by the FAC, published accuracy I believe is +-3kts due to AOA-sensor error. However in reallife probably more accurate.
You can easily 'manage' the speed when you have a discrepancy as the A/THR will fly the PFD(FAC) or FMGS(loadsheet) green dot/S/F whichever is higher. Only when in landing config the aircraft will fly the FMGS Vapp or VLS(FAC, speed-tape) whichever is higher, hence you will not always have a 5kt split. Some people do bump the Vapp up by a few knots.