If your grinder bit is too low or too high the diamond surface will not grind the whole of the glass edge. This can lead to chipping of the surface of the glass at the edges.
A good practice is to start with the bit as high as possible to allow for differing thicknesses of glass. As high as possible is with the bottom of the diamonds just below the platform of the grinder. This will ensure that you can deal with varying thicknesses of glass without immediate adjustment. You can then lower the bit as it wears.
Of course, you need to ensure there is adequate water reaching the grinding bit to avoid overheating the glass, and to keep the dust from grinding from getting into the air.