This is a pretty common problem with pickups using two magnets like the Gibson P-90. In your case, the magnets are not put back into the pickup right. What is important to remember is that each magnet has a South Polarity (S) and a North polarity (N). The same polarity (both South or both North) shoud face each other (they will repel each other). Normally Gibson P-90s have both South (S) polarities facing each other. The pickup has a metal spacer on the bottom, below the bobbin, that conducts the magnetic field to the adjustable polepiece (5/40 fillister head) screws. Both the magnets South (S) polarity faces the metal spacer.

To make the P-90s act like Humbuckers when both pickups are used, reverse the Hot and Ground wire on the neck pickup and flip over the two magnets 180? degrees. This will make the the pole pieces have a North (N) polarity. The two magnets North side face the metal spacer that conducts the magnetic field through the poles.