It's just occurred to me that Ruby might have undone some of the Doctor's past. In Empire of Death, the Doctor mentions he was in the Department of Health for the overthrow of Roger Ap Gwilliam. We can probably assume that was before the events of 73 Yards (Doctor time), but then in 73 yards Ruby overthrows Roger Ap Gwilliam all by herself (plus Old Woman, depending on how you interpret the ending). So it seems Ruby erased some of the Doctor's history in that timeline.