I took apart my bass, for fun(non humbucker sadly) and, noticed foam pads which press up the pickup when screwed down, moved a bit and messed up the angle and hieght of the pickup. it was visably fd-up i dont know if yours was so it could be something else. However, what i did to fix this was remove those pads put a dob of strong glue to them and arranged them to fit as normaly as posible, i think i even took some sissors and reshaped em' you could also add more pads to stablize the pickup better. press on the pickup see where it leans to. have fun
D class
May 2006