That might be a problem, That randomizer can seriously screw up the pokemon in it when you randomize everything. If I remember correctly you can randomize the stats of all the pokemon also so that Raikou you started with could have some seriously jacked up stats.
When I played emerald I used the old randomizer, I didn't know the universal one existed until I made that thread. All It did was randomize wild pokemon, same with the blue one I used right now. But back to the point That thing can even randomize the starting screen pokemon on red and blue, Do NOT challenge the Randomizer's Power.