The Super Tower /R, in it's original configuration is wired just as you mention. The 12 and 15" woofer are wired to the bottom binding posts, everything else is wired to the top posts. The crossover network allows them to be hooked up as you mention, with the 12 and 15 wired independently, or all drivers together. There is a toggle that enables you to switch between standard single amp and Bi-amp configurations.
It sounds like somewhere along the line yours were wired up differently/incorrectly? I make the the wiring sound simple, in actuality the crossover network is pretty complicated (at least to my untrained eye.)
Maybe someone has a diagram they can dig up for you.
Good luck!