Hi,
I tried to set new colors (sky, fog, water, grass and foliage) in different biomes (minecraft:beach, minecraft:swampland and biomesoplenty:grove) and I noticed some features working and others not :

Beach biome
New colors were applied for everything.
Swampland biome and Grove biome
Grass color and Foliage didn't show up.

I tested without ressource pack, and without Optifine.
Here is the code for the Swamp Biome (the same for all, just the ID changed) :
swamp = forBiomes(6)
swamp.set("grassColor", 5651200)
swamp.set("skyColor", 12976128)
swamp.set("fogColor", 2757888)
swamp.set("foliageColor", 5651200)
swamp.set("waterColor", 5651200)

I know about Swampland having hardcoded colors and the same for some BOP biomes, but I remember using a special ressourcepack with MCpatacher in 1.7.10 that overrided all the colors, according to a palette for the grass, for the foliage, for the water etc.

Minecraft 1.12.2
Forge version : 14.23.3.2669

BiomeTweaker for MC 1.12 is now EOL, so I will not be addressing bugs that are related to BT - MC interactions. If this bug persists in BiomeTweaker for MC 1.18, please submit a new issue.

Do you have BiomeTweakerCore installed and the relevant features enabled?

same

Yes and everything is on "true"

The script:
Tweaker.setStage("BIOME_REGISTRY")
Tweaker.createBiome("brushland")
brushland = forBiomes("biometweaker:brushland")
brushland.set("name", "Brushland")
brushland.set("topBlock", "minecraft:grass")
brushland.set("fillerBlock", "minecraft:dirt")
brushland.set("genVillages", "true")
brushland.set("isSpawnBiome", "true")
brushland.set("enableSnow", "false")
brushland.set("temperature", "1.5")
brushland.set("humidity", "0.1")
brushland.set("grassColor", "-4212907")
brushland.set("foliageColor", "-5331926")
brushland.addToGeneration("DESERT", 5)
brushland.addDicTypes("HOT")
brushland.addDicTypes("DRY")
brushland.addDicTypes("SAVANNA")
brushland.addDicTypes("SPARSE")

The chat log after running btinfo while in that biome:

[19:02:33] [Client thread/INFO]: [CHAT] Biome Status Report:
[19:02:33] [Client thread/INFO]: [CHAT] ID: 40
[19:02:33] [Client thread/INFO]: [CHAT] Name: "Brushland"
[19:02:33] [Client thread/INFO]: [CHAT] Resource Location: "biometweaker:brushland"
[19:02:33] [Client thread/INFO]: [CHAT] Class: "me.superckl.biometweaker.common.world.biome.BiomeTweakerBiome"
[19:02:33] [Client thread/INFO]: [CHAT] Root Height: 0.125
[19:02:33] [Client thread/INFO]: [CHAT] Height Variation: 0.05
[19:02:33] [Client thread/INFO]: [CHAT] Top Block: "minecraft:grass[snowy\u003dfalse]"
[19:02:33] [Client thread/INFO]: [CHAT] Filler Block: "minecraft:dirt[snowy\u003dfalse,variant\u003ddirt]"
[19:02:33] [Client thread/INFO]: [CHAT] Ocean Top Block: "minecraft:gravel"
[19:02:33] [Client thread/INFO]: [CHAT] Ocean Filler Block: "minecraft:stone[variant\u003dstone]"
[19:02:33] [Client thread/INFO]: [CHAT] Actual Filler Blocks: Check the output files.
[19:02:33] [Client thread/INFO]: [CHAT] Grass Color: "-7160487"
[19:02:33] [Client thread/INFO]: [CHAT] Foliage Color: "-8934609"
[19:02:33] [Client thread/INFO]: [CHAT] Water Color: "16777215"
[19:02:33] [Client thread/INFO]: [CHAT] Temperature: 0.8
[19:02:33] [Client thread/INFO]: [CHAT] Humidity: 0.4
[19:02:33] [Client thread/INFO]: [CHAT] Water Tint: 16777215
[19:02:33] [Client thread/INFO]: [CHAT] Enable Rain: true
[19:02:33] [Client thread/INFO]: [CHAT] Enable Snow: false
[19:02:33] [Client thread/INFO]: [CHAT] Dictionary Types: Check the output files.
[19:02:33] [Client thread/INFO]: [CHAT] BiomeManager Entries: {\n "DESERT Weights": [\n 5\n ]\n}
[19:02:33] [Client thread/INFO]: [CHAT] Spawnable Creatures: Check the output files.
[19:02:33] [Client thread/INFO]: [CHAT] Spawnable Monsters: Check the output files.
[19:02:33] [Client thread/INFO]: [CHAT] Spawnable Water Creatures: Check the output files.
[19:02:33] [Client thread/INFO]: [CHAT] Spawnable Cave Creatures: Check the output files.
[19:02:33] [Client thread/INFO]: [CHAT] Spawn Biome: false
[19:02:33] [Client thread/INFO]: [CHAT] Tweaked: true

And the biometweakercore.cfg file:

Configuration file

asm {
# This can be used to specify biome classes BiomeTweaker should not touch with ASM. You can find the class for a biome in the output files. You should only be using this if you understand what ASM is, and you know the issue it is causing. [default: ]
S:"ASM Blacklist" <
>
}

"asm tweaks" {
# Enables the 'addActualFillerBlock' command. [default: true]
B:"Actual Filler Blocks"=true

# Enables 'fogColor' in the set command. [default: true]
B:"Fog Color"=true

# Enables 'foliageColor' in the set command. [default: true]
B:"Foliage Color"=true

# Enables 'grassColor' in the set command. [default: true]
B:"Grass Color"=true

# Enables 'genInitialSnow' in the set command. [default: true]
B:"Initial Snow Gen"=true

# Enables 'oceanFillerBlock' in the set command. [default: true]
B:"Ocean Filler Block"=true

# Enables 'oceanTopBlock' in the set command. [default: true]
B:"Ocean Top Block"=true

# Enable this if you want BiomeTweaker to force topBlock and fillerBlock overrides in most biomes. This is done by using ASM to strip some assignments that happen in the 'genTerrainBlocks' method. This will not work for all biomes. This WILL cause issues where some biomes will have incorrect top and filler blocks if you do not override them (Extreme Hills (M), Mutated Savannah, Taiga). light ASM must be disabled for this to have any effect. [default: true]
B:"Remove Late Block Assignments"=true

# Enables 'skyColor' in the set command. [default: true]
B:"Sky Color"=true

# Enables 'waterColor' in the set command. [default: true]
B:"Water Color"=true

}