I am in a test world and put diamonds in the top slot of the Calcinator with coal in the bottom. The only output is dust.

1. Going to need to see a FML log
2. What version of mods are you using?
3. Hold shift and mouse over diamonds in your inventory. What does the tooltip say?

If a Calcinator is producing ash from diamonds it's likely because diamonds don't have an energy value associated with them in your install. I just tested using the latest EE3 and it produces Minium Dust just fine.

Odd, it is working now...

Did you use a fresh instance?
Maybe the DynEMC Thread was not done running yet, so Diamonds had no EMC value at the time?

It was not a fresh instance, the game had been running for about 30 minutes so the thread should have been running (plus the diamonds had EMC), and it works now. :-/