I think GameInABottle screwed up a bit there. Some shrines won't let you use all types of gems, the "special damage" won't do red, yellow, apparently orange, and maybe more... It's a weird thing. I think it was missed in the thought process. I suggest submitting a bug report at contact@gameinabottle.com and make them aware of it.
seriously, I tried to get the yellow, red, lime, orange and purple gem, of any grade, from grade 1 to grade 12, but it didn't work. so I hope this glitch will be solved soon. it doesn't look pretty those empty places, next to the places with the medals.
That's so weird!! I did the same thing, and all the gems I tried to place in the shrine did not work (pretty sure I tried orange, lime, and red). I hope this bug will get fixed!
I agree that it is hard to define the way a yellow or lime gem works with special damage as opposed to other gems, but I believe it is possible. I would make it so that there is a chance of triple damage on the set or a chance of an extra hit...but who knows. I'm not smart enough to program a game; I just play them!
Since there are so many Gemcraft 0 threads, and many on the subject of amulets and gems alone, please help us to consolidate the threads by posting further discussion in this thread. Thanks!