If you MDI a move does it go the right way? If so then its just your hot keys that are messed up and you can reset from Config menu then System Hotkeys. If it goes wrong from MDI then you likely have the wrong pins assigned for the axis in question.
Hood

I found the problem. I stupidly plugged the stepper cables into the wrong plugs on the Gecko G540. How do I set the limits on axis travel?

If you have Home switches then you can easily set up soft limits, they are accessible from Config menu.
You need to set X and Y min and Z max to Zero, X and Y max will be the amount of travel you have and Z min will be the travel but as a negative value.
You can then experiment with the slow zone by jogging at full rapid towards the limit to make sure it slows down quick enough to prevent the real limits being hit.

If you dont have Home switches then you will need to jog to the extent (or a known repeatable place) on your axis and press the Ref All button and you can then have softlimits as described above.

If your home position is other than X and Y fully negative direction and Z fully positive direction then you will need to set up a Home Off value equal to the distance that axis is away from that position.
Hood