She is probably leery of the puppy, which is a strange animal to her even though you've already had a dog. The puppy may just be too active and noisy for her.

If you can crate the puppy from time to time and bring the cat up and let her have a special treat close by, this may get her used to the presence of the puppy. Don't force the issue when the puppy is loose, however.
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Smile, it will make them wonder what you are up to!

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