I had this same problem with my 96 Honda Civic EX. Turned out in my case one of the wires going to the downstream O2 Sensor was cut by the heat shield, which was caused by a Rubber Grommet problem that looked like it was supposed to hold the wires away from the heat shield.

If you are having this problem, and the wires by the Intake Manifold look ok, make sure to follow the wires through the whole system.