Whenever I use the master infusion to craft essences together, the master infusion stone is consumed.

This was tested with inferium -> prudentium and prudentium -> tertium, in both a vanilla crafting table and a crafting station from Silent Gear.

Possible negatively interacting mods (subset of mod list):
RandomPatches, Just Enough Items, crafting tweaks

I removed FastWorkBench and it wasn't that.

Are you using the latest version of Cucumber Library?

We are using cucumber 2.0.4, and mystical agriculture 2.0.1
Apologies for not mentioning versions in my initial post.

Also, seeing now that there is a fix for my exact issue in cucumber 2.0.5, I'm happy for this issue to be closed; again, apologies for the wasted time.