…Scarily, all my other ideas are worse.
Okay, brace yourself:
If it can spread across all matter, why doesn't it seem to affect gaseous matter? If it does affect gaseous matter, why hasn't it simply absorbed and transformed earth's atmosphere? Can it affect liquids? Can it affect living tissue? Can it affect types of iron that are not Iron-56? What would blue-black fire do to that crystal that transforms whatever it touches? How is this distinct from said crystal? Is this thing connected in any way with the Church of the Broken God? Why is it a bad thing if the flame is suspended in vacuum, if it's not getting out of containment? Does the flame grow in size as it consumes matter? If so, are there any circumstances in which it would shrink? If not (to the last question), how would spraying iron-56 at it do anything other than keep it from spreading? How do you spray iron-56 anyhow? How big is the flame in containment right now?
Oof! That was a big one!
It does affect ages, which is why it rises and spirals in open air; it's spreading to the gas. It didn't kill the atmosphere because the Foundation got to it in time. It does affect liquids, which is mentioned in the description, and living matter…I don't see why not. Yes, it affects iron that isn't the 56 isotope. For the crystal, the fire would probably burn it into iron-56, and then the crystal's effect would turn it back into quartz after three hours. (Possibly an infinite loop.) The difference is that the crystal shrapnelizes after fully converting something, which lets it spread, whereas the fire doesn't and also works on gases*. It's not connected to the Church, unless someone wants it to be in a story or something. It's not a bad thing if it's in vacuum; misleading statement corrected. It spreads, so yes, it grows. It shrinks when it doesn't have adequate fuel, like a normal fire. The spray (dumping iron-56 powder on it) basically snuffs it out like a "fire blanket". in containment, it's down to about 1 in3.
Alright, I've taken this stuff into account, and patched the holes. Sort of like putting a bandaid on a sucking chest wound, but still.
*Yeah, this might not be enough.