Water contains oxygen, at a higher concentration than air. It will oxidize the aluminum at a higher rate than the surounding air. Result is what looks like a stain. Bare aluminum should always be dryed as soon as posible and for long term storage, like winter a wipe with wd40 on a rag will leave a protective grease film on it to protect it. Wax won't work on aluminum cause it has no pores for it to embed into. Once these spots show up, the surface material needs to be taken down to virgin aluminum again. If it's only minor 1500-2000 grit sandpaper and then blend the whole wheel in with that. Follow up with the polishing method of choice on the whole wheel. Bare aluminum is a pain, but with elbow grease and patience it can always, if not neglected too long be brought back to new looking condition, and sometimes better. If it's a machined looking finish, instead of polishing use a green scotchbrite pad. Ask the ole for one as it's a common item at the sink.
Ron

 

Maybe its a good time (winter) to get the stock wheels chromed

 

I really can't tell from the picture but it looks like what happens when you leave S100 Wheel Cleaner on too long. I would bet that is what happened at the Dealer when they washed it before you picked it up and the dummy that washed it left it on too long. I would go right back to the Dealer and show him!.

 

Sounds like a job for Never-Dull

 

Had the same issue, think its brake dust staining them, could not get the stain off but didnt really care as I was going to chrome them and did. I also switched to lyndall pads, almost no dust comes off them.

http://www.chromeprosplating.com/

Here are pics of the results

https://www.hdforums.com/forum/touring-models/292938-09-stock-rims-chrome-pros-pics.html

 

Blue Magic metal polish and 0000 Steel wool and elbow grease.

 

Take it back to the dealer! Sounds like the aluminum is oxidizing under the clearcoat or the clearcote has been pitted with something it didn't like. If soap and water won't take care of it - they'll probably need replacing. Better do it now - or live with it from now on!
No aluminum polish will help because it has a layer of clear paint on it, and you definately don't want to go down the polishing aluminum wheels path - a lot of work!

 

Brake dust is staining/pitting mine already to. I used Eagle One nevr-dull and it took it right off. I can't believe that the wheels are starting to pit slightly only after letting it sit for two weeks. THESE 09 WHEELS ARE A ***** TO CLEAN! I hate them.
Gary D.

 

Some clearners like 409 can stain aluminum, and there is a warning to that effect on 409 bottles. S100 can also stain if not washed off immediately, but I doubt if it'd do it to the extent you've experienced, and though I do use it I haven't seen any staining like that on the wheels. Recall what chemicals you've used on or near the wheel and tire.

Also, is the stain only on one side? Perhaps you have something leaking, although I'm not sure any oil or fluid used in the drivetrain would stain like that. Is there evidence of any oil on surrounding parts? You could also have run over some chemical on the road that had spilled out of another vehicle.

 

I remember when I first got mine and cleaned it up that there was a sticky film of something all over both wheels. I used all kinds of stuff to break it up and take it off but it was hard coming off. Brake dust really stuck to that stuff.
Gary D.