This was my set up, i disabled dye trees in normal biomes cuz i didn't want random color trees everywhere, i dunno if that has something to do with it. And i Left the rainbow trees to false as well, cuz i didn't care about them in the rainbow forest, and just wanted the dye trees. I have changed the rainbow trees to true now, just to see what happens. But you may be right about the world gen.
B:"Allow bonemeal on White Trees"=false
B:"Allow mod logs in Dye Trees"=true
B:"Console Loading Info"=false
B:"Debug Mode"=false
B:"Dye Block Particles"=true
I:"Dye Tree Density in Normal Biomes"=1
B:"Generate Anti-Taint plants in Rainbow Forest"=true
B:"Generate Dye Trees in Normal Biomes"=false
B:"Generate Rainbow Trees"=false
B:"Overworld Rainbow Forest"=true
B:"Rainbow Forest Biome"=true
I:"Rainbow Forest Biome ID"=90
B:"Rainbow Slimes"=true
B:"Retrogen Trees"=false
B:"Use vanilla dye items"=false
I:"Vanilla Dye Drop Percentage"=10
B:"Generate Rainbow Trees"=false This is now set to true