Finally I found the issue. When saving all contexts up to the persistent store, is used a method saveToPersistentStore:
that I used from RestKit
, with some minor changes to match our requirements.
The following line, that should work as a fix on iOS5, caused the issue, at least on iOS6:
[contextToSave obtainPermanentIDsForObjects:[[contextToSave insertedObjects] allObjects] error:&localError];
I have to further investigate wether the issue only occurs on iOS6 (right know, we are not targeting something else) before I send them an issue request, but simply removing this line fixed the issue.