I fixed it (through it's propably temponary fix).
Open palette editor in any level which doesn't use Custom Palettes. Choose FG Palette 1 and change Palette 2 Color 2 to black. Press Save RGBs to ROM. I tested this on Iggy battle. It's has small side-effects in the ground... but they are not visible in any tileset which haved FG Palette 1 displayed normally...