Angelo-
I took you to mean that the pickups weren't really "split" in the middle position, that this was wired as a std SG with both full HBs in the center switch position. If you have a coil split there, then yew's right, that could well be the problem.
No coil split, just standard HB's in center position. Maybe I am being too picky as it seems that the consensus is that some noise is possible with HB' as well.
Out of phase is out of phase, it doesn't matter what got it there or which way you fix it. The result of flipping the magnet or of switching the wires should be exactly the same.
I cannot recall why I went for the magnet flip. except that it worked... no Peter Green doinky tone.
Hum-cancellation is never 100%, even HBs can make some noise, and depending on windings and the vagaries of an individual set of pickups, you certainly could get more cancellation in the middle position with 2 HBs as compared to either one individually.
Ok if that's the case then I am just chasing a very subtle bit of noise.
The fact that you get the same amount of noise with either HB selected individually would seem to indicate the problem lies outside of the pups themselves- and noise issues can be devilish to track down, and even tougher for others to diagnose at a distance.
I don't have a "smoking gun" I can point you to here, just general principles. I assume you've done the basics- tried different amps, different cables, etc.- to eliminate causes other than this particular guitar.
If so, a double check of your connections is next- starting with the bridge ground and other grounds.
If all else fails, as JA points out on the original Gnutz site, sometimes HBs can benefit from shielding, although it's usually not needed.
Do you know for sure that this noise was not present originally, before you switched the bridge pup magnet around?