From what I gather in the half completed ops manual, this device reflashes on every startup with configuration info from the mach 3 customized xml file. Is this correct?
Is there something I need to do to reset this smoothstepper card  or is it faulty?  thanks

The SS does get reflashed each time you start Mach3.

I'm not sure what pins you are referring to on the SS being shorted. A resistor is usually only damaged by too much current, the SS board can't supply enough current through the outputs to cause damage like that though. If there were a short on the SS board, or something was wired wrong, etc then it may be possible. The best thing to do is contact Greg at Warp9 and send the board back. He will take a look at it and repair it.

alright will do. thanks.

This keeps getting more interesting all the time.  The pins used on the ss to drive the buggy z axis work fine on one of the other axes.
I diagnosed the drive board in question thoroughly, there are no shorts, opens, or other problems, the optoisolator currents for step and direction are 8mA and 7.5mW respectively, almost exactly what I had calculated they would be. No power supply shorts, no other interferences on th ez drive board I could find. 

So I removed the smoothstepper from the installation, reverted back to mach3 alone, and it works fine. As it always did.  The z drive simply opened its resistor for some reason but is now perfect again.  But the smooth stepper doesn't work at all.  It constantly trips out on emergency stop all the time randomly, and won't drive that z axis.  I don't understand it at all. 

Does it say "External EStop Requested" in the status line in Mach? If that is the case you just might need to adjust some of the SmoothStepper settings. Take a look here: http://www.soigeneris.com/documentation-content.aspx . Go to teh SmoothStepper section and downlaod the installatiuon tips PDF.

Correct, that it does...I will take a look.
But the head scratcher is...since this is open loop, no feedback to the ss gets back, so why when sending data to the z drive does it trip out, but not the same lines to a different drive when i swap it out to feed the x or y drive?   It has no way to know which drive it is feeding.

My suspicion is that something is wrong with your Z-axis drive that is causing enough noise to swamp the USB communication. The 'External E-Stop requested' message happens when the SmoothStepper is running out of data, if it sees the buffer is running low it will ask Mach to go into EStop mode. Setting the Controller frequency and axis frequencies properly will give you the largest buffer size you need for your set up (last page of PDF). If the problem is noise you are going to have to find the source of the problem.

You can try swapping the Z axis stepper motor for another one, in other words at the drive swap the wires going to to the X and Z axis. If the problem now occurs with X axis motor you know it is in the drive (the Z drive). Make sense?

You make an interesting point about noise...I haven't done anything during this troubleshooting to keep the USB cable away from the noisy interior of the controller box, in fact the box is open.   Will check these various things later this week, thanks for the assistance.  Maybe I should loop a carbon toroid onto the USB cable a turn or two.

A ferrite core will often help. The problem can also be noise getting back into the PC. I have a small fluorescent light above a workbench in my shop. If I turn it on/off it creates a large enough spike on the mains that it causes a spike on the DC power of the PC's USB ports. The USB keyboard/mouse will cut out briefly and the SmoothStepper will also drop out. I put a line filter before the PC/stepper control box and power the SmoothStepper with an external 5V power supply. If you have a scope you can take a look at the 5V on your USB ports and see if there is a problem.

Ok, I corrected a few things, and now all that's left to fix, is that ugly "External EStop Requested" which happens way too often when i jog the z axis.   Had replaced the z axis cable with a better shielded one, which corrected one problem.  The biggest thing was having the laptop anywhere near the controller box, noise is apparently a bigger problem than one would expect.   Get that USB cable anywhere near the box or the cables, and it trips out.  What besides noise, is the fix to this External Estop Requested issue?   Is it a data throughput error? What can I change to fix it?