JB/Jazz pickup combo - question

I *just* recently bought a new Ibanez S520. (Love it!) I decided to swap out the stock pickups for a Seymour Duncan JB and Jazz - HH combo. My friend wired it up. The bridge pickup has slightly less gain than the original stock pickup, but it sounds good in position 1. The jazz/neck pickup also sounds good. The problem is, positions 2, especially 3, and 4 sound tinty and boxey. I guess I was hoping the new pickups would sound at least as good as my ESP's Duncan Designed pickups. The ESP's pickups sound more balanced and more like they belong together. The new Duncan JB/Jazz hotrod combo sounds like the two outside positions (1 & 5) belong, but I feel like it's lacking a blend. Am I missing something? Is there a problem in the wiring? Is there a way to take these pickups and make them sound more blended? Forgive me, but "HAILP!"