What have you tried ? If you just put Z on it and have some spots(stains), Z6 should be able to remove them. Are you sure it's from the rain ? If you had spots on the car before the Z, then it may be "under" the Z.
I've had this problem as well. I seem to recall a few other threads with people having this problem as well. The water-stains on my Z'd Supra wouldn't budge until I removed the layers of Z. The marks were definetly in the layers of Zaino.