Sounds to me like you have an even amount of removal on one side, but the other is not touching flush...correct?
The term bevel means that the two sides are meeting in space at a sharp angle.
Like this /\ .

I think what you mean when you said the bevel set just fine on one side, is that it appears to be a consistent and even amount of removal or scratches on one side.

My advice at this point is to get a sharpie and color in the edge on both sides, see exactly where the metal is meeting stone.