If she checks out with the vet then this behaviour is usually a sign of stress, especially in a new mum.
Have a good look at her situation with the pups. Make sure she is in a private place and be very strict with visitors in the early days. She may be feeling insecure and is attempting to take a higher dominance in the pack to ensure her pups' safety and survival. Marking the "true" den area, the place where the "alpha" should sleep, suggests that she is reinforcing her ownership of the den and trying to increase security.
Oh - and - puppies do not calm bitches.
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