Hood:  I must be missing something, I'm not sure of what it is but I cant trigger the switch, and its probably because i don't know what to press, I've tried using the keyboard it seems to be the only logical place for me to try pressing the switch, when i do i don't get a prompt or anything.  My procedure is go to ports and pins hit the automated switch select the x home switch hit the auto select, i'm prompted that its searching, and asked to press the switch so i press the key board switch that corresponds with the limit i'm trying to set but nothing else happens. when i check the switches don't light.   I think i'm missing something in this process.  do you trigger the switch with the keyboard or is there something else i'm suppose to use.

Do you have physical Home switches on the machine. What I mean is actual switches attached on the machine that get triggered when the axis travels towards them and a ramp or similar contacts them.

Hood

CliffL
I will assume that you are also using the Y Home switch as a Limit switch and it sounds like you have a bouncing switch.
What would seem to be happening is the as Mach contacts the Y switch it then starts to back off but it sees the switch momentarily close and sets Home, the switch then opens and Mach then sees it as a Limit switch.
Try setting the debounce Interval (on General config page) to 2000 and see if that helps.
Hood

Hood, that worked great. Now I have set home at 4X 4Y -2Z. They do not go to the distance I have set.

The Home Off value is not for setting the distance, what it is for is to tell Mach how far away your home switch is from the extent of travel.
As an example you may have separate home and limit switches. The limits will be at the extent of the axes but the home switches may be in a bit from the end. The Home off value is then used to tell Mach how far the Home switches are away from the extent.
Hood

How would I set mach up to end the machine at 0-X 0-Y  0-Z.   Which technically is 6" X  4" Y and -1 for Z  After the machine touches all the limits and backs away for 0

Two things to consider with that question.
First is machine zero and work offset zero can be different, so it will depend on which you are talking about.

Second thing is, you should still be able to command a move to machine coords zero and not trip the limit switches. The reason for that is the zero position is set when the switches close after the homing routine reverses the axis. So unless your switches are prone to triggering by vibration then you should not trigger them with a move to machine zero.

Hood

No I don't have any physical switches attached to the table.  Also can you tell me why the object no longer lines up in the table display whats responsible besides the g code.

My limits are not prone to vibration. When I reference all  the machine comes to a stop at all limits and backs away from each about a half inch or just enough to open the switch. Which is what they are supposed to do - After they home the machine and then reset they become limit switch's. What I need to figure out is how do set that distance the machine backs off to - to be set where 0X 0Y 0Z is. I have a fence fastened to the machine so I can put a block of material in it - thus is is set at 0 - which technically is about 6" X - 4" Y these measurements are from the point where the machine touch's the limits to reference and then should go to what I call home.

I meant to say close the switch