Here you go. Thank you

You have your Y Axis step pin set as 13, that is an Input pin not an Output, that is more than likely your problem. Probably you should have it as Pin 8
Hood

thanks for your help, I'll let you know how it goes

Ok, Sorry It took me long to reply. I made the change and it made no difference. My machine is at zero location. When I click on ref y, The DRO for Y counter increases in the negative direction. but the axis it self on the machine does not move. I am trying to set the soft limits and I am getting an error of machine out of limits for softlimit activation. Please advise. Thank you

OK so to recap what happens when you Jog the X axis, does it move correctly?
Same for the Y axis, does it move correctly?
If you reference the X  it is OK?
If you reference the Y what happens?

For your softlimits issue it could be you dont have the Y axis referenced properly.
What happens when you press the Ref All button on the Program Run screen?

Hood

The manual at this link may help you with homing and limits, look in that section.

http://www.artsoftcontrols.com/forum/index.php?topic=3979.0

Brett

Also noticed Enhanced pulseing wasnt enabled in your xml that you posted. Enable it , it wont help with the above issues but usually helps overall, you will find it on the right side on the General config page.
Hood

Thanks Hood, I'll enabl enhanced pulsing.
to recap:
- When I jog x, x moves and when I jog y, y moves - no problem here
- When I ref x the y/a axis moves in the positive direction. When I ref y, the dro numbers increase in the positive direction but the y axis it does not move on the table.
- When I click on go to Z, all axis go to table 0,0
- when I click ref all, the y dro increases in the positive direction but none of the axis move on the table.
I posted 2 zip files under a different post (mach 3 strange behaviour). They have pictures of my machine and screen shots of my settings.
I also have a video that I can send you that shows the exact problem. it is 10mb file.