It can take some time and iterations to make the bed level.
Remember it is level with the tip of the extruder nozzle that is the goal, not level with the world.
I was leveling the bed all the time, and setting the z-axis endstop (fine control) all the time. Now that I have more experience, and have it set pretty well, I just check that the glass is flat against the heater board and print. It has been very stable now. I do remember working very hard to get the first layer height to work well in the beginning.