I had a similar thing with our previous cat. He would start wobbling his head from side to side, then flap his ears, then scratch furiously. The vet checked him and could find nothing wrong. She didn't think it was painful, just irritating to him. We found that good hard ear stokes, including round his neck and on the fur at the back of the ears, seemed to relieve whatever was irritating him. He had it for several years and it never went away, but never got any worse. Sometimes he would walk up to me with his head wobbling and sit down beside me, maybe he even was asking for the treatment? Who knows.....
As you've had your cat checked, I wouldn't worry too much. Try scratch/hard stroking the whole area for him.
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