Wrong 'presentingViewController'

Calling [self presentViewController:messageController animated:YES completion:nil]; doesn't necessarily use the vc you call this on to present the other vc. By default it travels up the vc-hierarchy and presents the other vc on the root view controller. That's why in your case the presenting view controller is a UINavigationController.

If you want to force your MainViewController to be the presenting vc, you have call:

[self setDefinesPresentationContext:YES];

on your MainViewController before presenting the MessageViewController.

Edit: In case someone else reads this: definesPresentationContext seems to be bugged or the documentation is wrong. See the comments below and Cocoa Builder

copy of my answer from this question

from Programming iOS 6, by Matt Neuburg:

On the iPad, when the presented view controller’s modalPresentationStyle is UIModalPresentationCurrentContext, a decision has to be made as to what view controller should be the presented view controller’s presentingViewController. This will determine what view will be replaced by the presented view controller’s view. This decision involves another UIViewController property, definesPresentationContext (a BOOL). Starting with the view controller to which presentViewController:animated:completion: was sent, we walk up the chain of parent view controllers, looking for one whose definesPresentationContext property is YES. If we find one, that’s the one; it will be the presentingViewController, and its view will be replaced by the presented view controller’s view. If we don’t find one, things work as if the presented view controller’s modalPresentationStyle had been UIModalPresentationFullScreen.

TL;DR
1. set definesPresentationContext to true on the desired presentingViewController
2. set modalPresentationStyle to UIModalPresentationCurrentContext on the desired presentedViewController