Storage shouldn't lead to pitting of the rotors. Like you, after a car wash I will notice that the rotors are orange with surface rust and, also like you, it disappears after the first use. I stored my car after driving it so that there was no surface rust on the rotors; 2 1/2 months later they are still shiney even though my car is stored in an unheated garage. I wouldn't worry about it.
Brad
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