could be the switches. check the Top Stack fuses in the kick panel. Top Stack is Nissan's name for the convertible assembly. Since the top's working, I'm reluctant to blame the fuses, but they should always be checked first.
the QW relays are shown in this picture. check those to make sure they're receiving and sending power.
Also, one last idea is to check the fuse for the power windows. The QWs are ran off the same fuse.