Repetier does not work on Z axis

When I am connected via USB to repetier.
I can move the x and Y axis.
But if I try to move the Z axis, even to home it, it starts moving down and does not stop until I shut it down.
System:
SKR Pro.
Dual endstops build.
I Use NC connections on the Z stop switches, so I have the software configured for -1 instead.
I home by going up.
I do have a 12 inch Z axis, but have my Z length on the machine set for that height.

Sounds like it thinks it needs to move off the homing switch but the switch state never changes. Can you test the switch is operating correctly and the controller is seeing the state change with M119?

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I Use NC connections on the Z stop switches, so I have the software configured for -1 instead.
I home by going up.

Are you building a LowRider or a MPCNC? The setup for homing is different between the two. But what what bother me most is that the problem seems to occur if you just move the axis. What happens if you send a direct move command from Repetier-Host to the control board? Something like:

G0 Z10

Does the problem occur? If not, does it move 10mm up?

From the touchpad, Home z works fine.
Connected to repetier while in the middle of the Z range, M119 Shows both Z axis switches as open.

From repetier terminal, I could send Z1 -50 and it moves down 50MM. but if I try Z1 - 25 after that (it should more up 25 MM, it goes all the way down.

using the buttons to move up and down do the same.

After homing from the keypad,
I did Z1 -50 (I home to the top) it goes down 50
But if I try Z1 - 25 (where it goes up 25, it goes down.
I tried setting 0 in there once and had similar results. and Z axis moves goes down and does not stop.
Seems to be working fine from touchpad, but I hope to use PC and USB
I would really like to use wifi like I do with my 3d printer and Octopi

Is it in relative positioning? Maybe it needs a G90?

You might also try M122

The weirdest thing is you said it works from the lcd.

@jeffeb3’s suggestion sounds valid.

Also, have you double-checked the Printer Setup in Repetier? It may have different assumptions about axis direction and homing switch configuration than the controller and screen.