We are testing the (Y) axis only and move onto the limit switch which is indicating in mach3's screen.
We then move off the switch and press Ref (y) to zero our position.

Next we manually move the (Y) away from the switch about a foot or so.

Then we tell mach to go back to our Ref position....by selecting ref all it shows on the screen counting back to our position
but the (y) axis is not moving back at all. We can move it using only the keyboard arrows or MDI commands.

If i goto MDI and type in G0 Y0 mach then works correctly by going back to it's home position.....

we have traced all the cables and the pins which are working.

When we manually hit the limit switch the indicator on machs screen is working.

What is seems like is that Mach3 is not seeing the values that we have set in the software settings...

Does mach need to have a Z home first before the others work ?  (this is a 3 axis machine but we have only setup the Y axis for
testing.

So what am i missing

If you disabel the z and x home switches in config, ports and pins, inputs. It should only home the y axis.

I have sent you a personal message.

Brett

We are testing the (Y) axis only and move onto the limit switch which is indicating in mach3's screen.
We then move off the switch and press Ref (y) to zero our position.

 I think you are misunderstanding what the Ref Y button does. When you Press Ref Y your Y axis should start to move towards you home switch, it will trigger the switch, mach will stop and then reverse until it sees the switch close, at this point Mach will then zero the axis and that will now be your zero position. However please note that this zero position is the machine coordinates zero position and you can set any position on the axis as a work offset Zero. So if you already have a work offset in the DRO when you reference the DRO might not show up as zero but if you toggle the Machine Coords button it will show as zero.

Next we manually move the (Y) away from the switch about a foot or so.

Then we tell mach to go back to our Ref position....by selecting ref all it shows on the screen counting back to our position
but the (y) axis is not moving back at all. We can move it using only the keyboard arrows or MDI commands.

The reason the Y axis wont move is because the Ref All button references the Z first then the Y then X. As you dont have any switch fitted to the Z (and I am presuming you dont have motors connected either) then it will keep moving in the DRO until you abort.
 If you go into your ports and pins and then Motor outputs and disable you Z and X axis you should be able to play around with your Y and get a feel for what is happening.

Hood

Forgot to add, the Ref buttons are not to move to your machine coords zero, they are for setting up your machine coords so that Mach knows where it is. You should only need to reference once on startup, that is unless you have a crash or some other error or stop the machine using the E-Stop , then you wil need to rereference.
Hood