You won't have the problem with the '97. With the '99 (and I think '00 and up) Honda wired 2 hot wires to the reg and 2 ground wires. If you look at the schematic, they join in the wiring harness so it must have something to do with the design of the Honda r/r.
Again, just plug the wires according to the picture in this thread, you'll be fine.
Mike how did you connect the black wire? I recently tried to use a 99 RR on my 97 but it didnt work so i thought it might be because the black wire wasnt connected to something