So far as I can tell, this could only happen if both the 'drive' and 'sense' matrices were inverted which seems unlikely given that boards and interconnection look to be manufactured in a way which would make this difficult to do, or it is simply that the boards are mounted in an orientation that is flipped 'end to end' from that intended.
If this is so, I think that HW would refuse auto-detect since it probably expects the bottom note to have a lower note than the highest.