This is a long shot but I figured I'd see if anybody else has seen/fixed this issue.
I have an pre-IOS 6 app that uses a UISplitViewController with NavigationControllers in both the master and detail pane.
In iOS 5 and earlier, if I push a UIViewController onto the master navigation controller, it slides in; popping that view controller then slides it back out.
In iOS 6, in landscape orientation only, if I push a UIViewController onto the master navigation controller it slides in; however, popping that view controller then appears to consider the viewcontroller modal because it centers the view controller in the screen and then drops it to the bottom like a "dismissModalController" command would do. If it is in portrait mode, it slides in/out as expected.
I'm not sure what to do about this - Newer apps with similar layouts don't have this problem. I suspect it has something to do with the initial window/navigator setup which (in this app) was configured the old way with MainWindow.xib and MainWindow-iPad.xib. I'd rather not try to rip all that out and reconfigure using the "new" way (which does it all in the appdelegate)