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I thought that the git plugin remembered the SHA1 of the preceding commit it processed so that it could use that earlier SHA1 to generate the list of changes. If the SHA1 of the preceding commit was in the Jenkins job, then was somehow removed, it seems like that might cause the failure you're describing.
Is there any chance the job moved from one node to another between the passing and the failing run?
Was the workspace wiped between the passing and the failing case? If it was wiped, then the plugin might remember the SHA1 which no longer exists in the newly cloned repository.