I am using an Ethernet Smoothstepper.

It's possible that the Smoothstepper plugin is the issue. I can test when I get home, but I suspect that it will work correctly with the parallel port.

I did some testing at lunch.  It does the same thing using feedhold then stop, hitting the e-stop or a hitting a limit switch. The common factor seems to be that I have to actually start running the program, then stop it.  It works fine even if I e-stop or hit a limit switch if I haven't started the program.  This evening I will try to figure out if one of the g-codes in my program is affecting this. I can stop it after running a few seconds and it does it, so it must be early in the file if that is the case

I'm using Vectric VCarvePro to generate the file.

I narrowed it down this evening a little bit.  Below is the file that I load.  If I e-stop the system on or before the M6 command, the auto-zero still works.  Anything after that seems to cause the issue.

( text1.5 )
( File created: Thursday, October 23, 2014 - 11:55 PM)
( for Mach2/3 from Vectric )
( Material Size)
( X= 6.000, Y= 6.000, Z= 0.125)
()
(Toolpaths used in this file:)
(Text)
(Tools used in this file: )
(1 = V-Bit {60 deg 0.125"})
N100G00G20G17G90G40G49G80
N110G70G91.1
N120T1M06
N130 (V-Bit {60 deg 0.125"})
N140G00G43Z1.5000H1
%

I thought I remembered reading about how to fix this, but I can't seem to find it.  When I hit TAB to pull up the diagnostics screen, it only comes across half way and most of it is hidden off to the right of the monitor display.  I can't drag the window over to see the rest.  Any ideas?  I think I'm running the original screen size (not the 1280 one).

Also, my z axis is on a really slow drive screw while my x and y can move very fast.  In the screenset, when I set jog to 25%, this is great for my x and y, but z jogging takes so long.  Is there any way to set z independently?

I switched to the Mach3_2010_inch.pp post processor and the problem went away.  Not sure why, but it works for me!

Thanks for the support.

I switched to the Mach3_2010_inch.pp post processor and the problem went away.  Not sure why, but it works for me!

Thanks for the support.

I had meant to ask you earlier, was there a message that probing was complete? I'm guessing there was.

Check your tool table, and see if you have a length entered for tool #1. If so, then what you were seeing was a tool length offset being applied.

I thought I remembered reading about how to fix this, but I can't seem to find it.  When I hit TAB to pull up the diagnostics screen, it only comes across half way and most of it is hidden off to the right of the monitor display.  I can't drag the window over to see the rest.  Any ideas?  I think I'm running the original screen size (not the 1280 one).

Do you have "Auto Screen Enlarge" checked in General Config? If so, you need to uncheck it.

Also, my z axis is on a really slow drive screw while my x and y can move very fast.  In the screenset, when I set jog to 25%, this is great for my x and y, but z jogging takes so long.  Is there any way to set z independently?

Afaik, Mach3 doesn't have independent jog rates.

Auto screen enlarge was unchecked.  Other suggestions?  Any other info I can give you about my settings that may help?

You have to grab it by the left edge to pull it over.
Do this:

Hit Tab.
Drag the left edge over.
Hit tab to close it.
Hit tab again to open it all the way.
Drag the left edge again.
Hit tab to close it again.

Close and restart Mach3 and it should stick.

If you really can't drag the left edge, then that's an issue that I've never heard of.