So why are the Madness Ore Matrices SOOOOOO prolific and the Amber ones are almost impossible to find?

Bad luck. It's as though you'll always find an abundance of the ones you don't want. Just go around in caves and loot Gnarls and maybe you'll get lucky.

Do more dungeon diving in Mania. I have multiples of all of them. And don't forget to drop them (I decorate my houses with these) as they are really nice to look at, especially the long, vertical ones.