It might seem odd that you have to break in a coffee machine but that is a common experience. I am not really sure why it happens. It could be oils on the surface of the boiler, group or the filter handle or perhaps a myriad of other things but it happens nevertheless. Obvious signs that the machine is not broken in are pale crema and possibly a quick pour. The single Rancilio basket is also a likely source. Forget about it and only use the double.
There are a lot of posts here about the subject. Some ideas:
What sort of coffee are you using? Is is a dry processed (i.e. "Natural" or washed. One of the reasons why DP coffees are used as the base for blends is because that add crema. There are other reasons too but your question was about the crema.
I assume the coffee is fresh.
Amount of coffee is another possibility. Put you measure in the drawer and try this. Completely fill the basket with coffee (i.e. overfill it), tap it on the bench to settle it. If it is lower than the top of the basket add more coffee then level it with a straight edge. Tamp very lightly and draw a shot. You are aiming at 60 ml in 25 to 30 seconds. If you get this you are on the money. Chances are you are not there. Adjust your grind to get the flow rate correct.
Somewhere along the way you will probably have found the missing crema. Most of us have been down the same path as you seem to be experiencing. These days I can get so much crema that it seems that is all there is and when it settles there will invariably be a 1cm layer sitting on a double.
Give it time and practise.