1. A method for diagnosing any combination of persistent and intermittent faults or intermittent faults in a system, comprising: obtaining a measured behavior of a system by measuring and/or probing the system at particular points; investigating a predicted behavior of a modeled system of the system by drawing inferences based on at least conditional probabilities, prior observations and component models of the modeled system; comparing the predictions to their corresponding points in the system; determining if conflicts and/or deviations exist between the measured behavior and the predicted behavior; adjusting the conditional probabilities to more and more accurately reflect action faults in the system, so they will accept a possibility that a subsequent measuring and/or probing will produce a different value or output; and using the conflicts or deviations between the predicted behavior and the actual behavior to obtain a final result based on a new value or output, wherein intermittent failures arise from a stochastic physical process which is intermittent at any level of abstraction of the system model, and wherein the intermittent failures diagnosed by adjusting conditional probabilities so that they continue to accept the possibility the subsequent measuring and/or probing will produce a different value acts to avoid irreconcilable inconsistencies in the system.