@THayes ,
Can you please make a few more pictures of the machine possibly also where which cables are located and where they are connected!
Can’t see where the cable is coming out on the x-axis. Since we can’t see it going across, it probably is correct.
-S
The connectors are not reversible, as that would reverse the power polarity, and destroy the Linear Module. The resulting smoke, and other issues, would be very noticeable. 
Also, if you don’t see the X-axis cable going across, it is clearly on the right side, as the cable is too short to not be visible if it is routed from the left.
@THayes ,
so definitely a case for support.
Unfortunately we can’t help you, at least I can´t help you.
I think the photos that @THayes shared show the position of the machine at the start of calibration, that’s why I thought the the cables are plugged into the wrong sockets.
Just an FYI, even if all of the axis are plugged into the wrong axis port of the Controller, they will still home to the exact same position. Z at the top, X to the left, and Y to the front. The only thing that changes is that the Linear Modules will home in the wrong order.
The new firmware may fault if it detects a 20mm lead in the Z, or if the lead of the X & Y does not match, but I haven’t test that.
It should but only if the latest firmware is installed, which in these types of scenarios often isn’t the case right out of the box.