Didn't have this issue at all until I began adapting my app for iOS 6. Whenever I return from a modal segue (with dismissViewControllerAnimated:completion:), my main view is shifted up by about the status bar's height worth of offset (and is subsequently behind the status bar).
The only workaround I've found is to add:
self.navigationController.view.frame = CGRectMake(0, 20, 320, 460);
self.view.frame = CGRectMake(0, 0, 320, 416);
to my dismissViewControllerAnimated:completion method (those values are for an iPhone < 5 and are just for explanation). But this doesn't really solve the problem, because when I go to present the next modal view controller, the presented view is then shifted up by about the status bar's height worth of offset.
No idea how this issue arose. My suspicion is that, somewhere in the segue, one of the navigation controllers loses track of the status bar's existence (linked to the new status bar, in some way?).
EDIT:
a screenshot of the main view, post-modal dismissal. [Note: 20px whitespace on the bottom]