Let me get this straight. You have a hive with two deeps, and they're not building out comb in the second one, right? So far this sounds normal to me. A package of 3,000 to 4,000 bees is almost the bare minimum to start a new hive. I find wild swarms I get have considerable more bees and do a much better job of building up. Two such swarms I've caught this spring actually need supers put on them now. Your package of bees actually sounds about right. They didn't have comb to start out with and it takes a while for the queen to get enough space to work her full potential of 2000 eggs a day or so. The result is you were only getting groups of new bees born in small spurts. They're the best for drawing out comb becuase they're not doing anything else in the hive, adult bees play the roll of foraging to much. A swarm of 20,000 bees or so has all of the bees participating in building a nest and usually build up much faster.
Sounds like you're doing good to me.