Explained:
When the osmium axe is on the crafting grid on the steve's workshop. It crashes and the axe is gone.
Crashed 2 times in a row and I think it is a bug.
Edit; Also, it is confirmed normal crafting table makes the same issue.
Edit; More confirmed: osmium shovel crashed on crafting table.

I'm reporting it here since it's refering to both the timeless ivy recipe function calling for a tool material on the mekanism tools and also calling on the mekanism tools functions. This is also being reported to aidancbrady (author of mekanism) as it also points to his mod

Test Enviroment: RR-3 Mainline Sandbox pack

Vanilla Crafting Table Crashlog: http://pastebin.com/y5E2Zp7i
Steve's Workshop Crashlog: http://pastebin.com/Lf6DB9uv

Neither, it's an external mod interfering.

Any ideas on what it could be seeing as you've encountered it before?

Dupe of #327.

Just want to ask, is this a problem on Botania's side of things or Mekanism's side of things?

Read the posts on the mekanism issue linked. Some mod is breaking the material checking code with stupid ASM.