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I submitted my app and Apple auto-rejected the binary as the entitlements were incorrect. After further research it appears that when compiling in MD 188.8.131.52 that it used the wrong distribution certificate in signing. It used the one for another app so I had to choose the specific certificate to ensure the proper entitlements (team/bundle) identifier were being set correctly. The team identifier for the other app was being used.
What was it originally set to? Automatic? Or was it set to the other certificate/provision?
It was automatic, when I set the cert specifically to my Distribution cert it actually failed to sign. I had to go into XCode 4.5 and remove the certs for the other app I'm developing so only my "Logbook Pro" app certs were available and that worked. It still used a different team ID but at least the entitlements for use of iCloud used the proper team ID for the app paired to the bundle ID.
I wanted to follow up with more details. I'm including screen captures of the binary details as seen in the app waiting for review in iTunes Connect. Notice how the different TeamID's are being used which I'm concerned may break iCloud now or with a later update if these change. My other app is called APDL and notice it has a different team ID from Logbook Pro which is the app now in distribution and waiting for review. I don't even have a APDL Distribution certificate created yet so the Automatic selection of signing certificate for Distribution in MD should only find Logbook Pro's info.
I originally had a problem which caused an auto-reject of the binary until I deleted APDL's certs from Xcode and then rebuilt and submitted Logbook Pro again. I tried selecting Logbook Pro Dist instead of Automatic and it failed to sign, my guess is an internal conflict with team ID's/Bundle Id's.
I would expect that the com.logbookpro....bundle id would be used to find it's associated cert in Xcode and therefore determine the correct team id. Also be advised that you cannot prevent the automatic team id from being attached to the entitlement if you were to enter it explicitly (teamid.bundleid) so I tried that and it failed.
Hopefully this is making some sense, if what I think is true above then I would suggest this issue may need to be escalated to "critical" if it could break iCloud sync and app submissions.
I've just implemented the logic to warn if multiple provisions end up matching the bundle id and signing key. I've also fixed the logic that collects a list of installed provisioning profiles to use the most-recently updated version of a provisioning profile if there are multiple copies of it.
Implemented filtering of Provisioning Profiles that do not match the app's specified Bundle Id, so that only valid Provisioning Profiles are included in the drop-down menu in the iPhone Signing Options panel.
This fix will be included in MonoDevelop 3.0.6