The human mind is conditioned to percieve the world in certain ways. You get used to seeing doors of a certain width, rooms of a certain height. If these proportions get thrown off in huge, obvious ways - for instance, by the vaulted ceiling of a Gothic cathedral - your mind can adapt. But when the rules are only bent slightly - when the ceiling is lowered by six inches and the doors are widened by about four inches - you feel something is off.
It's like a general case of uncanny valley, but with much fewer of the psychological issues concerning identity and such.