We use this form of words to show we are talking about a past action that is connected to another past action.
This is the ...ing form which we use to show that there is a period of time involved.
I had been painting the room for four hours when he rang. (Both actions are in the past (Painting and the phone call) they are connected and the painting was before the call. The painting took four hours and so we use the ...ing form.
I had been talking to him for an hour before he mentioned the money. (The talk and the mention of money are in the past and the talk started before the mention of money. We use ..ing because the talk lasted some time.
Why was the bus service cancelled?
It had been running late for years. (The late running is before the cancellation, connected to it)