I have been fighting this issue for days now and about to beat my head against the wall and put myself out of my code signing/app submission misery.
I have an application that has been submitted to the app store and accepted no problems (ver 1.0.0). I was able to publish the first update (ver 1.0.1) with a little bit of trial an error using XCode 3.2.4 and iOS 4.1 via Application Loader. Now I am on XCode 3.2.5 and iOS 4.2 and am trying to publish an update (ver 1.0.2) via XCode Organizer.
I can successfully build my application against the AppStore Distribution provision when I set my Bundle Identifier in the info.plist to "com.myCompany.myApp". But when I try to Validate/Submit the build via Organizer I get and error stating "Bundle Identifier: com.myCompany.myApp differs from prior bundle identifier ABC123XYZ1.com.myCompany.myApp". Apparently when I first submitted my app via iTunes connect I used the full (AppId).BundleIdentifer syntax. I have verified this by viewing the Bundle ID in iTunes connect.
So, logically, I added in the AppId prefix to the bundle identifier in the Info.plist file. When I do this and try to build again, I get "Code Sign error: a valid provisioning profile matching the application's Identifier ... could not be found." and the build fails.
I have tried everything I have read everything on the internet regarding these two errors with no resolution to the problem. I am in a catch 22 situation. I can't build the app with the AppID prefix in the bundle identifer and I can't submit it to iTunesConnect without it. Also, the iTunesConnect error occurs when trying to use Application Loader to upload the app.
I am prepared to offer my first born to anyone who can help me get out of this code signing/app submission hell!
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