Anybody got a xs650 with a stock charging system?

As the title says I need some help here.
On my XS (79)I have a custom wiring harness and the brown from the regulator connects through a fuse to battery. Well this fise blows when the key comes on.

After some testing I found that when the brown wire to the regulator has power it always sends power to the black wire and the green wire coming from the regulator.
Can someone test their working system and see if this is the case?

The black is supposed to be a ground, so I can't see why it would be hot.

Think of it this way, when you put 12V to a light bulb on one contact, and not actually ground the other side, the "other: side will show 12v. When you actually ground the other side, the voltage goes to 0 and the bulb lights up...

The regulator uses +12V Batt. and ground to reference the battery voltage. If you lift the ground wire off the chassis, it will show 12V.

However, if the internal diodes/circuits are bad, it could just be shorting out to ground.