Your reticle may not be perfectly square with the elevation knob - it may be slightly canted.
Rather then trying to level a scope to the action, I agree with others on the plumb Bob level. The plumb Bob's going to hang straight up and down (thanks gravity), and will allow you to get behind the rifle and level the scope and reticle to YOU, the shooter. Most people shoot with varying degrees of cant on the rifle, this way you are taking it out of the equation.
If you don't have access to a spot where you can hang a plumb bob, what I've done in the past that seems to work, when I had to level a scope and only had an apartment to do it in, is to take a cardboard box and place it against a wall. Will need about an ~10-11 yard distance if using an IOTA device, or longer if you have the distance and scope with the appropriate parallax. With the box in place, use a construction level and draw a cross hairs on the box with sharpie ( I prefer thinner tipped sharpies). Draw long lines, so you can use most of the reticle to level. Use a proper level, not some little rinky dink one. Get behind the rifle, setup as if you were to actually shoot (straight behind rifle, rear bag as you would use it, etc). It helps to put your scopes illumination on if you have it, and from here you can level your reticle.
Sounds ghetto, but it's worked well for me in a pinch when I've had limited resources and space to work with.