Im also curious about how the Z Axis is orientated too, when moving positively it travels upwards - the homing is set to minimum but when homing it searches upwards. Possibly this is because of the problems i am having with the Axis.

Thanks
It is usual to have the Z showing -ve going down so +ve and home would be at the top. The other two are personal choice.

Re the Z only moving in one direction check the (dir) on the driver and make sure it is changing sense ie 5v and 0v