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Panting is a way that dogs cool themselves off when they are hot and it can also be a sign of pain, anxiety or a signal of an endocrine problem or increased due to certain medication in addition to signaling respiratory problems.
Some breeds may be more prone to panting than others based on anatomy as well. What kind of puppy is she and how old is she?
I swear sometimes my dog pants when he is bored. As long as she is not in distress, I wouldn't be overly concerned about it. It sounds like she has been thoroughly checked out and has passed with flying colors. If there is no cause that can be identified, then I would just continue to monitor her. She may be more likely to pant under stressful conditions (i.e. when company comes over, during a vet or grooming visit, etc.).
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If there seems to be a worsening during certain times of the year or in different environments, you may consider a trial of diphenhydramine (Benadryl) to see if there is an allergic component. Since there is not evidence of anatomic issue or medical issue with the lungs, it may be that she is panting to help move air through a thicker than normal mucus secretion.
Benadryl is dosed at 1-2 mg per kg. You can round up or down to the next capsule or tablet size. The biggest side effect is sleepiness and sedation.