Staggering the gas rings is a popular bit of misinformation stemming from the assumption that these rings must work as piston rings in an engine. The fact is, once inserted into the carrier and seated, the gaps are negligible. If the tension from the seated rings will support the weight of the carrier (cam pin removed) then the rings are not the problem. Also, according to the factory, the rings have a tendency to move around a bit during operation so carfully spacing the gaps is all for naught even if it made a difference.
If you want to test for your weapon short stroking, load 1 round in a magazine and chamber the round. If the bolt locks to the back after that one round, the weapon isn't short stroking. If it is, you most likely have a gas system problem. Check your carrier key first (small tube on top of carrier that fits over your gas tube) It should be rock solid tightened and staked to the carrier. Any movement at all can cause short stroking. Beyond that, the gas tube is the most likely culprit. Make sure that it is straight, and that the roll pin that secures it in your front sight runs through your tube, not in front of it. If it does not run through the proper hole, the gas port will be at least partially blocked, and the function will be negatively affected.
One last possibility is ammunition. Did the ammo you are using previously work on this upper / barrel combo? Will a hotter load work as is?
I tend to agree with Bear Hunter, your lower is not at fault. In fact, I can't imagine a scenario that would fault your lower with the problem described as long as your fire control function test passes.
Let me know if that helps. If not, I'll see what else I can dig up.
Saleen