anchor: If it had been Inglethorp who was carrying on an intrigue with Mrs. Raikes, his silence was perfectly comprehensible. 
positive: If there had been an affair occurring between Mrs. Raikes and Inglethorp, Inglethorp's silence was completely understandable.
negative: It was incomprehensible that Inglethorp should remain silent, if he had been having an affair with Mrs. Raikes.