Speed values are more of a persistent value for Speed commands. If your S value is 0 and your spindle still spins a little, then the VFD further setup.
You can increase the value of P4-13 for the minimum voltage input for a speed command. This will make a bit of a deadband in the case of residual electrical noise. I would set my spindle speed to 0 and then check voltage at AI1 this value should theoretically be zero. If you have voltage there, set P4-13 to the number you see on your multimeter, this will create a deadband from zero to whatever number you insert causing your spindle to stop moving.