Well, it goes away with multiple hard brake applications, so I'm thinking it's just surface rust. It's not warped, just unevenly corroded
The longer I let it sit between drives, the more & harder stops I have to do to get the thumping & pulsing to go away.
clencher: in the past I've bought replacement rotors from the store that came with some kind of light waxy coating (which I assume is for rust prevention), but it would obviously be a pain in the *** to re-coat the rotors after every drive!