Update (2013/7/8) - This has been fixed in newer versions of iOS. However, it's worth knowing about if you're targeting iOS 6 or below.
You can blame Apple for this one, and it's actually pretty mean of them. Technically, backgroundColor is not customizable through appearance proxies.
From Apple's documentation:
To support appearance customization, a class must conform to the UIAppearanceContainer protocol and relevant accessor methods must be marked with UI_APPEARANCE_SELECTOR.
If we go into a class like UIBarButtonItem and look at the tintColor property we see this:
@property(nonatomic,retain) UIColor *tintColor UI_APPEARANCE_SELECTOR;
So because it's marked with the UI_APPEARANCE_SELECTOR tag we know it works with UIAppearance.
Here's where Apple are particularly mean: in a UIView, backgroundColor has no appearance selector tag, but still works with UIAppearance. According to all the documentation Apple provide it should not, but yet it does!
This gives the misleading impression that it will work for all sub-classes of UIView, including UITableView. This has come up before, in this previous SO answer
So the bottom line is that backgroundColor shouldn't work at all with UIAppearance, but for some reason it does on a UIView. It is not guaranteed to work on UIView subclasses, and it doesn't work at all on UITableView. Sorry I couldn't give you a more positive answer!