I have always used Mother's metal polish or Never Dul. I have removed water spots that have been on metal for over a month. My buddy had the same problem and we found out the raw aluminum was stained from road salt. The polish's were removing the water spots but it would of took 5 hours per rim, wasn't worth it in my book.
I haven't used they're products yet but they are inticing and i might give it a go. I am expierencing the same issue with my polished calipers. I used mothers metal polish with elbow greaes to remove most of the spots but i feel i need something with a bit more bite. I've heard Flitz isn't too good.
Have you tried Meguiar's Gold Class All Metal Restorer or their Professional Series: All Metal Polish? I had tremendous luck using those products to restore my aluminum fishing boat.
Here is a link to my gallery with the boats before and after shots: