I think you still have a very small amount of air trapped in the master cyl pump itself right between the where the reservoir feeds into it and the port that is covered when the piston moves the slightest. The air doesn't get pumped down into the lines because there is so little actual fluid flow in the braking system. When you first pull the lever it feels fine but the air is sucked into the piston port. When you grab it again, the air is now in the port so it feels soft. To get it out, you must aggressively bleed the pump. Take your time and pump a LOT of fluid through it. The air may be so small that you won't even see it escape, but I think it is definitely in there...