I went out and looked at mine. The dark blue wire goes to the "F" side (right/passenger)and the black wire goes to the "R" (left/driver) side through that two wire connector at the alternator. I still have the original type separate regulator if that makes a difference.

Just for the heck of it, make sure they weren't also reversed at the regulator, so all is well except the colors. If someone made a mistake at the regulator, the quick solution might have been to change it at the alt. Wierd stuff happens.