The doctor thinks it's acid reflux? Have you had any tests done? Do you have any allergies or asthma? Did anything bring this on three months ago, like a cold, stomach flu, food poisoning, or something? Do you take any other medication? Some medications can cause acid reflux or coughing. Has your diet changed?
If your acid reflux is not under control, there is a test. It's called a barium swallow test. You drink this stuff and then they take an x-ray while you are tilted upside down. I know it sounds weird, but it will show if you have any acid coming up. If you don't, then your cough is most likely caused by something else. If you do have the test, ask your doctor if you should go off the acid reducers to see if you have GERD at all (unless that has been confirmed already).
If it's not acid reflux and your primary care doctor is out of ideas, you may consider going to an Ear, Nose, and Throat doctor.