Re-wire on Gibson Les Paul Studio

This Les Paul had an issue with the wiring plus the owner wanted to get rid of the coil tap. I suggested it would be easier and cheaper to replace the modern wiring harness for the more traditional four pots and a couple of resistors. Worked out fine apart from the pickups where out of phase? I double checked the wiring and it was fine. Only thing I could think was they did this on purpose as Gibson’s coil tap isn’t really a coil tap, anyone know the answer to this?