In the first one, the actionis not complete, whereas in the second it is. Let me get some context for you:
1 Ustedes me estaban dando más dinero cuando entró el atracador
1 You were giving me more money, when the robber came in
2 Ustedes me estuvieron dando mas dinero durante el primer trimestre y ahora no quiero devolverlo 2 You were giving me more money during the first forth and now I don't want to give it back
Both actions are in the past. in case 1 it is not completed when another action occurs, in 2 the action precedes (or follows ) another action in the past, or present and it has been completed.