<p>I thought “had been running” would be correct because in writing questions we have to assume that anything not underlined is completely correct and there is no other way of making the sentence sound correct without taking the “had” out.
By the way, I do not agree with “had been running” being less common. Both past simple and past perfect tenses have their own specific uses which should not be mixed. By using “had been running” or the past perfect tense in the sentence, sense of continuation of an action which had ended in the past is conveyed.</p>