This has always been a sire spot for me. I HATE rusty header pipes. Stock headers will rust as well as stainless. The heat is what does it. If you notice it get nicer as it goes back. There is no way to prevent it. Even if you take it off and clean it with a wire wheel it will look like shit in a week. Your options are 1. Clean and BBQ paint it black. 2. Get a titanium header 3. Have the stock header jet hot coated. I will be doing this to my 09 crf. 4. You can header wrap it. Personally I like the look of a nice clean header pipe.
08 KTM 200xc
06 husky 510 smr (mine for now)
cr500af aka satan's supermoto chopped up
07 sxv 5.5 "meatball" sold
09 crf450r sold