Ah, the one I posted prior was 1 volume / 1 tone and 5-way switch selector.
Here is a 2 volume / 2 tone and 3-way switch
http://www.seymourduncan.com/support...h_2v_2t_3w_ssp
See if your directions line up with that.
Also, if you want to take a peak, here are more options:
http://www.seymourduncan.com/support/wiring-diagrams/
I'm not much of a pickup guru. But what you are saying does make sense and it does sound like a phasing problem. (mixed up wires)
When I installed my SH-6 Distortion, I remember that I had to tie two wires together (maybe red and white) -- but that would be different because it was a 1-volume.