Weird Crash after Upgrading to 3.5.2

I started working with my project after upgrading to Xcode 4.3.2 and Unity 3.5.2 and I'm having a really weird crash. When building and running I get this:

 -> registered mono modules 0xd3f270      
  -[AppController applicationDidFinishLaunching:]: unrecognized selector sent to instance 0x1d53c10    
  Terminating app due to uncaught exception 'NSInvalidArgumentException', reason: '-[AppController applicationDidFinishLaunching:]: unrecognized selector sent to instance 0x1d53c10'

It looks like UIApplicationMain(argc, argv, nil, @"AppController"); is calling the deprecated :
-(void) applicationDidFinishLaunching:(UIApplication*)application**

instead of:
- (BOOL)application:(UIApplication*)application didFinishLaunchingWithOptions:(NSDictionary*)launchOptions

I verified this by copying the applicationDidFinishLaunching method from AppController.mm that I had in and old build and remmed out the didFinishLaunchingWithOptions method that was already there. The game launched and worked but having to hand edit the AppController.mm file makes me really nervous about what else might be wrong.

Does anybody have any clue what might be going on? This is a fairly mature project that had been working. I have the SDK set to the latest 5.1 and the target was set at 4.1 but I changed that to 4.3 to test (no difference).

Thanks,
Geoff