doghouse wiring

I tried to use scan tool auto xray 5000. It would run a koeo scan but not a koer. E-mailed auto for any suggestions but had none. I did notice that of the five wires on the connector that only four matched the scanner. The scanner has 1,2,4,5,6 on the van it has1,2,3,5,6. Could it be possible that one of the wires on the van plug is in the wrong place. It has been scanned several times in the past.