Structure and Function of the Anal Glands in Dogs
If your puppy had trouble with his anal glands, you'd probably know. This has never been a problem for any of my dogs, but I hear anal gland secretions stink to high heaven--which makes sense, based on their purpose.
I'm scratching my head on how crating him in a clean crate is causing your puppy to stink.
I think you got me. Maybe other RDNs have insight.