Homing and Limits have been set and when I press Reference all Home everything goes home just fine in the picture on the machine. It is a fixed gantry so I wanted home to be in the X-, and Y+ and Z+, this way it would be the easiest to load and remove work.
When the machine has been homed and Soft Limits is activated I can drive the X in the plus direction and the Z in the minus direction, however I cannot move the Y in the minus direction. The only way I can move the Y in the minus direction is to disable the Soft Limits.
I have attached a screen shot of the Homing and Limits setup screen showing the settings; hopefully this will show where the problem is.