Well if you are doing them across the fall line you have to be using your knees. You need to bend to get the pop to do the rotation.
That said your upper body was rotating prior to you popping from the ground so that twisted your knee a bit and when you sprung up may have been when you heard the pop.
No Dr. here obviously but it sounds like just a small sprain or out of alignment pop, kinda like when you crack your knuckles.
As to the knee pads it's I doubt you damaged your knees from that but definitely sounds uncomfortable. I have used McAdams football knee pads in the past and these have worked well.