Is it possible to see SQL output in Console window ? The one that XCode is printing out when specifying '-com.apple.CoreData.SQLDebug 1' in scheme ?
you can specify program arguments in Run | Edit Configurations... | Program Arguments field.
Normally, program argumens should be imported from your existing schemes.
If this doesn't work, please file a bug report and attach a small sample project here: http://youtrack.jetbrains.com/issues/OC