The argument to appearanceWhenContainedIn: represents a view (and/or view controller) containment hierarchy, not a list of possible containers. (Admittedly, the docs aren't clear on this. See the video from WWDC 2011.) Thus,
[UINavigationBar appearanceWhenContainedIn:[NSArray arrayWithObjects:[MyViewControllerBase class], [MyViewController1 class], [MyViewController2 class], nil]]
gives you an appearance proxy for a UINavigationBar contained within a MyViewControllerBase, which in turn is within a MyViewController1 inside a MyViewController2. I'm guessing that's not the containment hierarchy you have.
Instead, look at the view controller which contains your navigation bar. It's probably a generic UINavigationController... but you can't just do
[UINavigationBar apperanceWhenContainedIn:[NSArray arrayWithObject:[UINavigationController class]]]
because then you'll get the mail/message controllers too. And sadly, while you can get at the appearance proxy for a UINavigationBar within a mail/message view controller, there isn't a way to tell it to undo appearance changes made at a more generic level.
It looks like the usual solution to such scenarios is to make yourself a UINavigationController subclass, and use it for the parts of your UI you want skinned. The subclass can be empty -- it only exists to identify parts of your UI for appearanceWhenContainedIn:. (Meanwhile, things like MFMailComposeViewController continue to use the default appearance because they still use the generic UINavigationController.)