Just took my DD to the dr this week for the same, had been waking with night coughing, already does Zyrtec and Flonase. We got a diagnosis of asthma (sadly) and a new inhaler, which has helped tremendously.

You need to get mattress allergen coverings. I don't care if she tested negative to dust. Get the anyway. Her symptoms are worse at night. Also, get new pillows and allergen casing for pillows.