I fixed the issue, it was a rather silly issue...basically was how dwarf fortress read the new line characters compared to how my program was writing them.
Some stones generated from the program, I had it generate 12800 stone types for testing ^^
Generated stone stats for 12800 stones
Magma Safe: 7505
Flux: 732
Igneous intrusive layer: 35.1484375%
Igneous Extrusive layer: 15.3203125%
Sedimentary layer: 34.53125%
Metamorphic layer: 13.9921875%
Metamorphic flux: 108
Ocean: 1383
Ocean shallow: 688
Ocean deep: 695
[INORGANIC:ORTIZITE]
[USE_MATERIAL_TEMPLATE:STONE_TEMPLATE]
[STATE_NAME_ADJ:ALL_SOLID:ortizite][DISPLAY_COLOR:0:7:0][TILE:138]
[STATE_NAME:ALL_SOLID:ortizite]
[IGNEOUS_EXTRUSIVE]
[IS_STONE]
[SOLID_DENSITY:2404]
[MELTING_POINT:11173]
[INORGANIC:BSITSTONE]
[USE_MATERIAL_TEMPLATE:STONE_TEMPLATE]
[STATE_NAME_ADJ:ALL_SOLID:bsitstone][DISPLAY_COLOR:7:0:1][TILE:132]
[STATE_NAME:ALL_SOLID:bsitstone]
[SEDIMENTARY]
[IS_STONE]
[SOLID_DENSITY:2414]
[MELTING_POINT:12764]
[INORGANIC:STRINGERITE]
[USE_MATERIAL_TEMPLATE:STONE_TEMPLATE]
[STATE_NAME_ADJ:ALL_SOLID:stringerite][DISPLAY_COLOR:0:7:0][TILE:137]
[STATE_NAME:ALL_SOLID:stringerite]
[SEDIMENTARY][SEDIMENTARY_OCEAN_DEEP]
[IS_STONE]
[SOLID_DENSITY:2916]
[MELTING_POINT:12163]
[INORGANIC:GERMANYIAN]
[USE_MATERIAL_TEMPLATE:STONE_TEMPLATE]
[STATE_NAME_ADJ:ALL_SOLID:germanyian][DISPLAY_COLOR:7:7:1][TILE:134]
[STATE_NAME:ALL_SOLID:germanyian]
[IGNEOUS_EXTRUSIVE]
[IS_STONE]
[SOLID_DENSITY:2050]
[MELTING_POINT:11898]
[INORGANIC:NEWTATE]
[USE_MATERIAL_TEMPLATE:STONE_TEMPLATE]
[STATE_NAME_ADJ:ALL_SOLID:newtate][DISPLAY_COLOR:7:7:1][TILE:138]
[STATE_NAME:ALL_SOLID:newtate]
[METAMORPHIC]
[IS_STONE]
[SOLID_DENSITY:2057]
[MELTING_POINT:11265]
The program is for a project I am working on, as I wanted a completely generated world from creatures all the way down to soils. I currently have the creature generation more or less done, it just needs some final tweaking to make the creatures less like abominations ^^. Along with metals, minerals, stones, plants, gems, smelter reactions, entitys etc, just needs some final tweaks and testing before I release to the public.