Halt causes jerk movement

Using PCI-7344 and MID-7604 and FLEXMOTION.
3-Axis control, stepper motors, closed loop with optical linear encoders.
1) When I am stationary and command a Halt, there is a resulting jerk movement, sometimes up to a few 1000 servo steps. Why?
2) The MAX PID Tune does not work at all. Is there a way to use the LabView PID VIs, including the Auto-Tune VI to tune the PID parameters? Do you have an example or documentation on how to do this?
3) I am having trouble with getting the move complete to complete. I realize one factor is the PID parameters. I have attempted to tune them manually with the Capture and Read Trajectory data (this is a very cool tool) but so far am not very successful at finding the correct PID parameters. Can I get more documentation on what factors are included in the move complete.
4) The pull-in moves at the end of the move do not appear to be limited by the commanded velocity and acceleration. Using the high rate data, I am often seeing velocities 4-5X the defined velocities, which then would throw-off the PID controller. Is this a design flaw? Why is this? The pull-in moves are usually completely un-successful at correcting the endpoint.
5) I am using a 3-D contour move to perform a curve. To define the geometery of the move, I need about 170 points. I would like the speed of this move to be approx 6000 steps/second. Due to the definition of the speed of a contour move to be dependant on the following parameters:
1) Distance between points
2) Time delay between points, limited to intervals
of PID rate which can be btwn 10-45 msec for the
fastest PID rate, or btwn 10-90 msec for slowest
This requies me to have a contour defined as 3500 points. This is a big drain on the system due to this restriction.
1) Why is this restriction here? Is there an work around?
2) When you change the PID update rate, what does that effect? High speed capture rate? All card processing?
3) There does not appear to be a way in LabView to change the PID rate? Am I missing it?

http://forums.ni.com/t5/Motion-Control-and-Motor-Drives/4-AXIS-MOVE-VI/td-p/58560

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