It seems that this is due to new code to do with the splash screens that has been implemented in AppController.mm which causes a side effect such that the didRotateFromInterfaceOrientation never gets called and as a result QCAR never sets up the orientation correctly.
One thing to note is that this does not appear to happen on iPads, just iPhone only.
Until this can be fixed at the Unity end, one approach you might like to try is to modify AppController.mm by commenting out the following lines in the shouldAutorotateToInterfaceOrientation method
// code before
[INDENT]bool requestPortrait = (targetOrient == portrait || targetOrient == portraitUpsideDown);
if(requestPortrait != _splashPortrait)
_splashShowing = true;[/INDENT]
// code below
This seems to eliminate the problem on iPhone and leaves the iPad version unchanged (i.e. still working as before), so it should give you the expected behavior.