If you have a particular gem that you wish to increase (such as raising a chipped ruby to a flawed ruby) then this trick is for you.

1. Find a gem shrine, but dont click on it.
2. Then put the gem that you wish to increase in your inventory, but make sure no other gems are present in you inventory. It would even be smart to remove any items that you are wearing that contain gems.
3. Then when you have everything above finished click on the gem shrine.
4. The gem that you had in your inventory will be on the ground but it will be increased .

For example: If you had a flawed ruby in you inventory and you clicked on the gem shrine, you flawed ruby will be changed into a ruby!