I can right click it with a Ruby Axe. Not sure if it is specific to Amethyst or Shovel.

Well then do more testing before reporting, if you're not sure.

I'm sure that it doesn't work with an Amethyst Shovel. That should provide you with enough direction. I don't really care either way as it's not enough of an annoyance to hinder game play.

I'm just reporting it to you in the event that you want it fixed, if so do your own research.

I don't in any way have anything to do with Blue Power. I'm sorry that my answer came out as rude as it did.
All I wanted to suggest with my reply, was that it would be nice of you did further testing, to figure out if it was related to amethyst or to shovels.

This is an issue with Applied Energistics. No shovel will work with a crafting terminal.