If you tell us what those “mixed results” were, or even better post an image, then we might be able to offer suggestions. A description of your process would help too.
Generally speaking a visible light led laser won’t damage glass, directly, it goes straight through.
If one side is coated and the diode color or frequency (nM) and it’s absorbed by the color of the glass backing, you can remove it, taking a little glass with it. You can use dark coatings or a piece of paper under the glass to do indirect engraving.
If it’s a coating on the glass, such as a mirror, top or bottom usually doesn’t matter, it’s kind of the wrong tool for glass.