Just downloaded the upgrade onto my iPad retina and noticed that my left margin is now indented. Maybe 1/4 inch. It is the screen itself, not just the margin for the words. The screen now is lined up under the "a" in iPad in the top left corner.
Don't know if I will try the updated on my iPhone 5 or not.

I also have this same finding. About 15 pixels.
The navigation bar is full width, just the text page is moved to the right.
Ipad v4 latest OS

I did try it on my iPhone5 and this is not a problem on that device. So it seems to be only on iPads.

Mr Burggraf figured out how to reproduce the problem last night.
Here's when the screen indents: launch the program with iPad in horizontal mode and the Home button on the left side of the screen.
Here's when it does not indent: launch the program with the the iPad horizontal and the home button on the right side of the screen, or launch the program with the iPad in portrait mode.
Check this out and see if you agree.
I wanted to pass this along to you so that you can cope with it till he gives us the fix.
:)