Intermittent Transformer Problem
Whether you are checking a switch mode power transformer, flyback transformer or inverter transformer, always keep in mind that those transformers can develop open or shorts a few turn when it gets warm. This kind of problem is rather hard to check because by the time you place your tester (ohmmeter to check for open circuit or Blue Ring Tester to check for shorted turns) on the transformer pins the result that you can get can be good. Do not worry about this because this kind of problem does not happen so frequent as compare to semiconductor.
If you have a set of equipment for repair and you suspect that the transformer is the cause of the problem but the transformer is tested ok (and all the corresponding components also tested good) your only choice is to direct replace the transformer and retest the set. You got to make sure the related components are all good because it is not easy to find the exact transformer.