The lens is only a guide, and as you see it's not accurate in all cases. Generally, it's fine, but the problem is that the base NWN gameassigns values based on item properties and such. For those custom items like our various gems that were not in the original game, we've assigned a value, but NWN the game sees a "Gem of True Strike" or whatever and does not know it was based on a particular stone and should thus be worth more than the stone.
If you think they're worth more, charge more, just keep it within reason. Though I'm not sure how many people will pay 800 for fine feldspars, but hey...it's worth a shot, right?