Hey, I've been tryin to play through gemcraft chapter 0 for a few days now (i must say it's a lot harder than the previous one...) and the day it came out, the shrines stopped workin for me! if i tried droppin a gem bomb, it wouldn't do anything. the gem would just go back to my inventory (yes, i checked to make sure i had the gem bomb "spell" pressed). Usually, when i would go to drop a gem bomb on one of the bolt shrines, it would show how many bolts it would fire and how much damage it would do. It doesn't say that when i'm hovering with a gem bomb over it. it just says "Charges __"
yeah when using shrines they don't have to be gem bombs, and I don't even think they are would work if the gem bomb button is pressed. As M3T4LH33D said just drag them into the shrines.