I had this problem a few weeks ago with my rear xtr v's. When the pins are in the centre holes, the pads line up to the rim nice and square as you say, but there is no spring.
I had to use the top hole and adjust the pads down. It doesn't look right but the brakes work well. Just takes a bit of messing to get the pads in line.
Has anyone been able to get v brakes to work with pins in the centre holes? This is certainly the way that looks right as pad adjustment is much easier
On the back side, the arm has a metal little bar comming from the mounting of the brake. That bar (spring-arm) needs to be hooked on the outside of the brake at the pin. Now it is on the inside and doesn't give it any tension.