I havent had that problem on a bike but have on cars. I believe that means your starter has shorted (if I remember right it is the windings) or the relay between the start switch and the starter. The pos side melted because it was pulling so much amperage. When you fixed it with a new cable (less resistance) then the neg probably started going because it was full bore through the starter...
Anyway I think that is right, it's been a long while thankfully. Hopefully it did not do any other damage.
I would start by checking relay then checking the resistance or take starter to a good electrical motor shop to have them check it.