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PJ Wiring Question - Wires Reversed

I replaced the P pickup in a PJ bass (Squier P bass Special) with a Quarter Pounder and wired it up as indicated in the wiring diagram - white to the middle lug of the pot and black to ground on the back of the pot. After putting everything back together, each pickup played alone sounded fine, but together the sound was weak and sounded out of phase. I then reversed the connections from the new P pickup, with the black going to the middle lug and the white to ground, and now everything seems normal. My question is this - should I leave well enough alone or is there some reason that I should fix everything so that the black goes to ground and the white to the pot? I suspect the original J pickup is wired wrong, but it may be something else. Any ideas? Thanks.