Then that's a problem. You'll have to go through your config files and give them all unique IDs, keeping in mind the ±128 thing. I believe that the available IDs range from 0 to 255; the ones used by Vanilla can be found
here. Yes, it's painful and annoying and there really should be some way to automate it or at least tell you if there's an overlap, but there's really no other way to do it. And then you might have to regenerate your world, or at least use something like MCEdit to delete and regenerate the chunks with the wrong dimensions' biomes.
One of the things I like about Reika's mods: He explicitly crashes the game on loading if anyone tries to use one of his biome, enchantment, or potion ID. I'm not sure if he checks for conflicts between other mods as well, but you could try installing DragonAPI to check. Just don't load up any worlds if you intend to remove Reika's mods later; that can cause (fixable) problems of its own.