I'm having this problem now. Just tried to start playing Factorio again after months of not playing, loaded a save which I'd barely gotten started on from older versions and upgraded it, unlock the crusher, and I can't "smelt" stone.
Old versions:
base: 1.1.32
Krastorio2: 1.0.23
New versions:
base: 1.1.39
Krastorio2: 1.1.5
flib: 0.8.3
factorioplanner: 1.1.25
I also tried disabling factorioplanner and reloading the save and same result.
Any help would be appreciated!
In the meantime, I'll try starting a new game from scratch and will see if that achieves anything...
Edit: New game from scratch (without factorioplanner) still results in "stone cannot be smelted".