Homing X and Y can't jog after homing?

I will take a look at this tomorrow, thank-you.

I just checked and it moves exactly .001 in both x and y but won't move anymore after that.

ok that pretty much confirms my hunch.
Either your axis directions are backwards on x and y or your homing directions are backwards.

Looks like you are using shared both limits and homing, so there is no way for linuxcnc to know if you homed towards the wrong side.

Can you describe your machine or show a picture. My guess is the tool moves up and down but the table moves for x and y?
If so when you press the positive X jog key, the table should move left.
Positive Y the table should move towards you.

Is that true?

When standing in front of the mill, positive x goes to my right, positive y towards me. The table moves.

ok fix the x direction.
Then as for homing which way do you want it to travel searching for home?

ie, usually I think y would home with the the table moving towards you.

Ok so I have managed to get the homing all sorted out except after all 3 axis homes the x and y axis won't move when I try jogging them, the z axis jogs no problem. I'm wondering if it's not coming off of the limit switches far enough but I can't seem to find where to change that. If Infact that is the problem?