Board Thread:Skyrim/@comment-109.77.27.101-20130729163834/@comment-11344160-20130731030846

That is really weird. It could be a glitch, but it's not one I've ever heard reported before.

Try putting your amethysts into a container and then leaving the area-cell (like, through a door that causes a loading screen). Then return, take your amethysts out of the container, and try smithing again.