Well, Clomid actually blocks estrogen (it is similar and so it replaces your body's natural estrogen), and then when you stop taking it, your body rebounds and releases a big rush of estrogen. In fact, Clomid has such a negative effect on estrogen that many people actually have to TAKE estrogen when they're on Clomid.
IMO the reason why Clomid/soy causes such bad O pains is because more eggs are coming closer to maturity.