Stuart, From your .ini file : MAX_VELOCITY = 12 or 15 inches/second? That is 720 or 900 IPM. Can the machine really do that? You don't show pid.0.output, it would be useful to see if the PID output is saturating. (It probably is.) I think Chris is right, the servo, at least set up the way it is, is not able to deliver such acceleration. 20 inch/second^2 sounds like a lot of accel to me, but then I'm not that familiar with high-end machines. There may be an option that changes the current limit of the servo amps in different modes, like turns up the permitted torque/current limit after homing is complete. You might check the motor current when the servo is accelerating to see if it is at the rated peak current for the motor.
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