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Even when the person seems to be doing it as a polite way of letting me know they are listening carefully,
In addition it means; I'm understanding what you're saying so far. As opposed to the signals that the listener is confused or does not understand the the current point you're making.
Un huh, is an important signal in conversation/communication. It signals that it's ok for the speaker to continue because the listener is following and understanding. Other signals tell the speaker that the listener wishes to interject a question or comment. Without un huh and the will-you-pause signals, the give and take in conversation can't function. What occurs without the signals is not conversation; it's a one way lecture.
Would yes or yeah be more tolerable signals for you to hear while speaking than un huh? If so, you might explain your aversion to un huh and suggest to your intimates that they substitute the yes signal.