I too have this problem and listening to my heartbeat drives me mad when trying to sleep, especially if it skips about. I have researched this online and find that it can be a side effect of some anti arrhythmia medications, in my case, Flecainide. It seems to be Hobson's choice! If you are not on any meds, then it would be best to discuss with your doctor.
I am not an expert on this but to me it seems like the common cause of pulsating pain is some kind of inflammation. Have you tried NSAID? You might have an ear inflammation or just wax in your ear. Otherwise, what I have read is that when your blood vessels become old and bad you stop feeling the pulse in them. So the fact that you can feel a strong clear pulse means that your blood vessels are probably young and healthy:).
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