It sounds like one coil is out of phase with the other in the humbucking pickup. Basically take one coil and reverse the leads connected to the second bobbin. If you are using a mini-toggle switch or it has 4 conductor wire make sure that you are using the correct wiring chart for that particular pickup. Most companies that make pickups use the same color coding but some use their own which makes pickup wiring a guessing game at times. Also make sure the bobbins are both wound in the same direction and both finishes are hooked up together. Then make sure the beginning of one bobbin is grounded and the other is hot. If the pickup sounds great by itself and now is out of phase with another pickup, reverse the ground and hot beginning wires coming out of the pickup.