Y-Axis..homed or not?

Hey folks,
We have recently assembled our M1000 and we are having an issue when we home all axis. As you will see from the images of the machine it is homed, and a screenshot of the controller software showing both y and z axis at 0 but the y axis at 1043 (limit of the y axis as opposed to 0).
We are desperately keen to get our machine up and running (we are using it in an education setting) so any help would be hugely appreciated.
I asked this question on the Stepcraft FB page and someone has responded telling me that when the machine is homed it should be showing this. Any CNC I have ever used previously referenced home as 0 on all axis so this would be a new one for me.
Any help would be much appreciated!
Thanks