I tracked down the bug in iOS 6 related to the display not adjusting to device rotation. This is a bug in PhoneGap and has been present since 1.9.0 with almost no progress. I tried some of the suggested fixes but none have helped. I understand the issue is related to the plist however currently I use the Build service to package my app since it’s easier. If issues like this keep coming up though I will just build locally.
In the meantime, the best I can suggest is update to iOS 7 if you can or bare with me while I attempt to get assistance from the PhoneGap Build team. Thanks!