I'm experiencing exactly the same thing, having to re-use a plist file generated from Xcode5. Just one other thing to add: The validate button, that we're presented with after archiving, does not validate my App correctly. It gets past "Preparing Archive" but then throws up an error, "No matching provisioning profiles found for Applications/plumbsApp.app" - None of the valid provisioning profiles allowed the specified entitlements: application identifier, beta-reports-active, keychain-access-groups.
Now, dismissing this and continuing with the "Export", creates my .ipa file and my users are able to install correctly, with the correct url, of course. So, not totally sure why this is happening. I had the beta release of Xcode running but used the final release of Xcode6. Perhaps the beta, comment, in red-herring. Has anyone else experienced this, where the validation of the archive fails in this way but the App installs ok?