I'm not sure if this is the problem, but for the PRS wiring to work properly the pickups need to be magnetically out of phase with each other (if wired in "normal" 2 humbuckers in parallel mode, which isn't an option on the PRS rotary switch, AFAIK).
If you order a pair of BKPs for a PRS, I believe Tim normally flips the magnet in the neck pickup.
You could try swapping the connections of the red and black wires of the Nailbomb, as that will change which coil of the pickup is switched off in each "split" position. But I think you'd also need to turn the pickup itself "upside down" for everything to work correctly.
Or I could be on completely the wrong track.