I am setting up a new KX1 mill. The Y axis homes properly by hitting the switch and backing off but the X hits the switch and stops with no backing off. Help!

Usually a sign of a bouncy switch, try setting a Debounce Interval of 2000, its on General Config page. If that helps then best solution would be to get another switch as debounce is really just masking the problem and not curing it.
Hood

I don't think its the switch. When I home and hold the y switch down it reverses the direction and zeros the axis when I let go. In X when I manually hold the switch down it just stops and never reverses direction.

If the switch is bad it will momentarily trigger then release then trigger then release etc etc etc, you may see the LED stay on in the diagnostics page but Mach itself is much faster than the screen graphics so you will not see it switching on and off.

Hood

One sure fire way to know if it is the problem is if the X DRO zeros in machine coords when the switch is hit.
Hood

When the x switch is hit the DRO keeps running because it is waiting to be released. But since the axis is not reversing it is not being release.

Ok so the switch is not being seen by Mach at all then, double check you have it set correctly in Ports and Pins and also look on the diagnostics page to see if you get the X Home LED lighting.
Hood

Set the debounce to 2000 and one of the switchs on X will cause it to reverse and zero and the other switch wont even though they are basically wired to the same input (Mach shouldn't know the diferance between the two) The screwy thing is after the X resets the value of Y the changes for no reason.

X homeing LED working fine

Please attach your xml

Hood