A muffling-spell is a magical procedure which prevents its victim from speaking out on a particular subject. It does not, however, silence them physically. Instead, when the victim attempts to speak upon the forbidden topic, the rational sentences formed in their minds come out of their mouths as a stream of inane babble. The gentleman with the thistle-down hair takes the precaution of applying a muffling-spell to both Lady Pole and Stephen Black when he enchants them to pass each night with him in Faerie. By this simple means he prevents both from alerting anyone to their plight, and consequently both undergo the torment of being unable to explain, even to those dearest to them, the change in their bearing and circumstances. Lady Pole's wild attempts to do so win her the character of a madwoman; the more stoic Stephen bears his burden in silence.
"A muffling-spell" is the terse diagnosis John Childermass offers when he meets Lady Pole at Starecross Hall. There he witnesses for himself her strange simultaneous existence in two separate worlds, and her equally strange inability to speak rationally in our own. Mr Segundus has already told him he sees a red-and-white rose before her ladyship's lips. Mr Segundus knows it is not a real flower but he cannot explain what it is. Childermass can: his extensive reading in magic tells him that roses are a sign of silence. He instantly sees what has happened to her ladyship, recognises the exact sort of spell she labours under and understands why, as a consequence, she is confined as a lunatick.
Interestingly, Childermass himself does not see the rose - he sees something quite different - he sees Lady Pole both as she is in Faerie, and as she stands before him in Starecross Hall. This is evidence of his great sensitivity to magic.