Is it your first time fighting him.. or what.. and did you fight Entei first? i fought Entei and got him, Raikou and him aswell, on Second fight. (After Story Line) aswell as Suicune, on Second fight, after storyline.
if you dont have the other two, that can be why, but can also be a reason for being its Recruite Rate is Dead Low. and i just lucked out.