In the printer settings, the two value is switched. In the figure the D value is the Height but on the 3D view the depth changes the Y coordinate.
System configuration:
* Windows 8.1
* Repetier Host version: 1.5.6
* Normal printer (coreXY)
Images: http://imgur.com/a/6r0eO</div><div><br/></div><div><br/></div>