Some classes have passives that buff certain types of damage. For example, as a Sorc, I get more damage from a Lightning glyph than a Flame one. Dunmer have higher fire damge racialy, and DKs also have bonuses to fire damage, I believe. It's likely stuff like that making the difference you are seeing.
SquareSausage wrote: »I cant remember tbh but I think I noticed that the glyph strength went down when I removed points from master at arms cp passive in the blue tree. So id imagine Elemental Expert would do the same?
Did you remove CP from there?