I've been doing some modding (evidently) and I've worked over a few areas. I've added or modified creatures, plants, metals, weapons, armour, stones, layers, and reactions.It was all going fine until one test, as it appears that all non-layer stones do not appear. Most gem clusters seem to appear with no problems, but not a single 'matgloss_stone_mineral' entry will work. I checked the errorlog and fixed a few basic errors (GORING over GORE for example) but nothing else appears amiss with the rest of the text. There are definitely no duplicate entries.
The 'reaction_all_economic' file looks like it might have something to do with it, but given that it doesn't even include all the default stones anyway, it might be nothing.
Check:
Stone Layer file is clean.
Unrecognized Stone Token: OBSIDIAN
Unrecognized Stone Token: HEMATITE
Unrecognized Stone Token: LIMONITE
Unrecognized Stone Token: MAGNETITE
Unrecognized Stone Token: GARNIERITE
Unrecognized Stone Token: GOLD
Unrecognized Stone Token: SILVER
Unrecognized Stone Token: COPPER
Unrecognized Stone Token: MALACHITE
Unrecognized Stone Token: GALENA
Unrecognized Stone Token: SPHALERITE
Unrecognized Stone Token: CASSITERITE
Unrecognized Stone Token: PLATINUM
Unrecognized Stone Token: TETRAHEDRITE
Unrecognized Stone Token: BISMUTHINITE
Unrecognized Stone Token: ALUMINUM
Unrecognized Stone Token: KIMBERLITE
Unrecognized Stone Token: BAUXITE
Unrecognized Stone Token: CINNABAR
Unrecognized Stone Token: COBALTITE
Unrecognized Stone Token: GYPSUM
Unrecognized Stone Token: TALC
Unrecognized Stone Token: JET
Unrecognized Stone Token: PUDDINGSTONE
Unrecognized Stone Token: PETRIFIED_WOOD
Unrecognized Stone Token: GRAPHITE
Unrecognized Stone Token: BRIMSTONE
Unrecognized Stone Token: REALGAR
Unrecognized Stone Token: ORPIMENT
Unrecognized Stone Token: STIBNITE
Unrecognized Stone Token: MARCASITE
Unrecognized Stone Token: SYLVITE
Unrecognized Stone Token: CRYOLITE
Unrecognized Stone Token: PERICLASE
Unrecognized Stone Token: ILMENITE
Unrecognized Stone Token: RUTILE
Unrecognized Stone Token: CHROMITE
Unrecognized Stone Token: PYROLUSITE
Unrecognized Stone Token: PITCHBLENDE
Unrecognized Stone Token: BORAX
Unrecognized Stone Token: OLIVINE
Unrecognized Stone Token: HORNBLENDE
Unrecognized Stone Token: KAOLINITE
Unrecognized Stone Token: SERPENTINE
Unrecognized Stone Token: ORTHOCLASE
Unrecognized Stone Token: MICROCLINE
Unrecognized Stone Token: MICA
Unrecognized Stone Token: CALCITE
Unrecognized Stone Token: SALTPETER
Unrecognized Stone Token: ALABASTER
Unrecognized Stone Token: SELENITE
Unrecognized Stone Token: SATINSPAR
Unrecognized Stone Token: ANHYDRITE
Unrecognized Stone Token: ALUNITE
Unrecognized Stone Token: COAL_BITUMINOUS
Unrecognized Stone Token: LIGNITE
Unrecognized Stone Token: OBSIDIAN
Unrecognized Stone Token: DEPLETED_SLAG
Unrecognized Stone Token: DEPLETED_SLAG
Unrecognized Stone Token: DWARVEN_CEMENT
Unrecognized Stone Token: DEPLETED_RUBBLE
Unrecognized Stone Token: DEPLETED_RUBBLE
Unrecognized Stone Token: DWARVEN_CEMENT
Unrecognized Stone Token: CINNABAR
VARISCITE: Environment Spec Stone Not Found, Token - BAUXITE
CHRYSOCOLLA: Environment Spec Stone Not Found, Token - MALACHITE
TURQUOISE: Environment Spec Stone Not Found, Token - KAOLINITE
BLACK PYROPE: Environment Spec Stone Not Found, Token - KIMBERLITE
DEMANTOID: Environment Spec Stone Not Found, Token - CHROMITE
RED PYROPE: Environment Spec Stone Not Found, Token - KIMBERLITE
RHODOLITE: Environment Spec Stone Not Found, Token - KIMBERLITE
DIAMOND_LY: Environment Spec Stone Not Found, Token - KIMBERLITE
DIAMOND_FY: Environment Spec Stone Not Found, Token - KIMBERLITE
RUBY: Environment Spec Stone Not Found, Token - BAUXITE
SAPPHIRE: Environment Spec Stone Not Found, Token - BAUXITE
FLAWLESS_OBSIDIAN: Environment Spec Stone Not Found, Token - OBSIDIAN
FLAWLESS_JET: Environment Spec Stone Not Found, Token - JET
Unrecognized Stone Token: DEMON_SOUL_SLAG
Unrecognized Stone Token: DEMON_HEART_SLAG
Unrecognized Stone Token: OBSIDIAN
Unrecognized Stone Token: HEMATITE
Unrecognized Stone Token: LIMONITE
Unrecognized Stone Token: MAGNETITE
Unrecognized Stone Token: GARNIERITE
Unrecognized Stone Token: GOLD
Unrecognized Stone Token: SILVER
Unrecognized Stone Token: COPPER
Unrecognized Stone Token: MALACHITE
Unrecognized Stone Token: GALENA
Unrecognized Stone Token: SPHALERITE
Unrecognized Stone Token: CASSITERITE
Unrecognized Stone Token: PLATINUM
Unrecognized Stone Token: TETRAHEDRITE
Unrecognized Stone Token: BISMUTHINITE
Unrecognized Stone Token: ALUMINUM
Unrecognized Stone Token: KIMBERLITE
Unrecognized Stone Token: BAUXITE
Unrecognized Stone Token: CINNABAR
Unrecognized Stone Token: COBALTITE
Unrecognized Stone Token: GYPSUM
Unrecognized Stone Token: TALC
Unrecognized Stone Token: JET
Unrecognized Stone Token: PUDDINGSTONE
Unrecognized Stone Token: PETRIFIED_WOOD
Unrecognized Stone Token: GRAPHITE
Unrecognized Stone Token: BRIMSTONE
Unrecognized Stone Token: REALGAR
Unrecognized Stone Token: ORPIMENT
Unrecognized Stone Token: STIBNITE
Unrecognized Stone Token: MARCASITE
Unrecognized Stone Token: SYLVITE
Unrecognized Stone Token: CRYOLITE
Unrecognized Stone Token: PERICLASE
Unrecognized Stone Token: ILMENITE
Unrecognized Stone Token: RUTILE
Unrecognized Stone Token: CHROMITE
Unrecognized Stone Token: PYROLUSITE
Unrecognized Stone Token: PITCHBLENDE
Unrecognized Stone Token: BORAX
Unrecognized Stone Token: OLIVINE
Unrecognized Stone Token: HORNBLENDE
Unrecognized Stone Token: KAOLINITE
Unrecognized Stone Token: SERPENTINE
Unrecognized Stone Token: ORTHOCLASE
Unrecognized Stone Token: MICROCLINE
Unrecognized Stone Token: MICA
Unrecognized Stone Token: CALCITE
Unrecognized Stone Token: SALTPETER
Unrecognized Stone Token: ALABASTER
Unrecognized Stone Token: SELENITE
Unrecognized Stone Token: SATINSPAR
Unrecognized Stone Token: ANHYDRITE
Unrecognized Stone Token: ALUNITE
Unrecognized Stone Token: COAL_BITUMINOUS
Unrecognized Stone Token: LIGNITE
Unrecognized Stone Token: OBSIDIAN
Unrecognized Stone Token: DEPLETED_SLAG
Unrecognized Stone Token: DEPLETED_SLAG
Unrecognized Stone Token: DWARVEN_CEMENT
Unrecognized Stone Token: DEPLETED_RUBBLE
Unrecognized Stone Token: DEPLETED_RUBBLE
Unrecognized Stone Token: DWARVEN_CEMENT
Unrecognized Stone Token: CINNABAR
VARISCITE: Environment Spec Stone Not Found, Token - BAUXITE
CHRYSOCOLLA: Environment Spec Stone Not Found, Token - MALACHITE
TURQUOISE: Environment Spec Stone Not Found, Token - KAOLINITE
BLACK PYROPE: Environment Spec Stone Not Found, Token - KIMBERLITE
DEMANTOID: Environment Spec Stone Not Found, Token - CHROMITE
RED PYROPE: Environment Spec Stone Not Found, Token - KIMBERLITE
RHODOLITE: Environment Spec Stone Not Found, Token - KIMBERLITE
DIAMOND_LY: Environment Spec Stone Not Found, Token - KIMBERLITE
DIAMOND_FY: Environment Spec Stone Not Found, Token - KIMBERLITE
RUBY: Environment Spec Stone Not Found, Token - BAUXITE
SAPPHIRE: Environment Spec Stone Not Found, Token - BAUXITE
FLAWLESS_OBSIDIAN: Environment Spec Stone Not Found, Token - OBSIDIAN
FLAWLESS_JET: Environment Spec Stone Not Found, Token - JET
Unrecognized Stone Token: DEMON_SOUL_SLAG
Unrecognized Stone Token: DEMON_HEART_SLAG
Unrecognized Stone Token: BAUXITE
Unrecognized Stone Token: BAUXITE