OK, reading back in the thread, I just wasn't certain that we actually got an answer on that, so I apologize for being redundant.
If the circuits test OK from end to end, there are other possibilities. One is that one of the CKP wires is grounded, and this wouldn't show up as irregular if you are using an ohmmeter to test from end to end. The wire can be connected at both ends, AND be touching ground somewhere, and if this happens, it will kill the CKP signal. Careful inspection of the wiring might reveal this, and you can also use an ohmmeter to test continuity to ground on the 5v and the sensor return circuits, they should NOT have continuity to ground in any fashion.
It's possible that the wires are broken right at the connector, this happens occasionally, and when you unplug it to test it, it makes the connection, but breaks the connection when you plug it back into the CKP.
It's also possible that your ECM is faulty, though this is a lower probability. ECM's are pretty high quality. I suspect a wiring issue, and just a careful visual inspection might reveal where this wiring is touching ground.