My horse has had them for over 8 years. Since the day I met him.
His old owners said they were from an ill fitting saddle.
I had an old friend tell me that they could be shaved down to the skin during fall when their winter coat was growing in, then with help of some vitamin E oil they should grow back it's normal color.
Personally, I would not do this to mine. We ride too much and shaved spots would make riding uncomfortable. However, it may be something to look into if they bother you that much.
How big are the spots? Pictures?