When shooting with live view, image quality degrades as the sensor heats up. This is just a guess as to why the first lens might be producing excellent results, and following lenses poorer results
Another issue is that you need to place the target closer with the 40mm lens than with the 70-200 because the AF sensor needs a sufficiently large target relative to the field of view of the lens. Usually it is positioned at a distance that is a fixed multiple of the focal length, like 50x (which would be 2000mm or about six and a half feet).
5DIII, 5DII, 7D x5, 6D, T2i, T3, 1D X, 10-22mm, 16-35mm II, 18-55mm II, 18-135mm IS x2, 70-200mm f/2.8L II, 24mm f/1.4L II, 50mm f/1.4, 50mm 1/1.8 II x2, 85mm f/1.8 x2, 100mm f/2 x2, 135mm f/2L x2, 200mm f/2.8L II x2, 1.4X III, 2.0X II, 60mm f/2.8 Macro, etc. only had room to list a few Canon items