Ah. Well, at least that's not a mod problem, then.
I've started playing around with the various crystals, mithril and levisium. So far everything is working out ok, although I'm testing to see what happens when you have a material with a negative density. So far all I've discovered for sure is that it doesn't throw any errors. Might have caused a crash when quitting, though, so that needs more testing.
General notes so far:
Tempered Crystal is a bit worse than bronze or wrought iron, as expected. Better than copper, though, so still a decent choice if you've got nothing else to work with.
Blood Crystal is ok for armor but quite good for bladed weapons. Not as good as steel, but better than bronze or iron.
Night Crystal is good armor and ok weapons. Except for flails, for some reason, which slaughtered everyone who wasn't wearing steel. Not sure why, so that needs more tests. Kind of cool, though.
Mithril is pretty awesome, weak only to Steel Mauls, which seems to get through it pretty easily (even Breastplate and Greaves). Mithril hammers and maces probably suck, need more tests there.
Levisium is...weak. Which is intended, since you're supposed to alloy it with other stuff for the weight reduction. However, it needs more testing since I didn't see any particular benefit to wearing it when I took over the various arena dwarves. Agility still made a much bigger difference than whatever armor I was wearing. So, lots more testing to do there.
I also haven't even started work on the alchemy aspects. But that can get done after I have the end products working properly.