I was diagnosed with GERD 2 months ago. One of my symptons was a terrible cough. I was put on Pantoloc (Protonix) for 2 months, and was recently put on Nexium. The cough had subsided (but not totally disappeared) with the Pantaloc, but since I have started the Nexium (about 4 days ago) the cough has been more harsh. I guess my GERD has to get use to the new medication.
The cough is always worse while you sleep because you are lying down making the acid in your stomach easier to get to your throat and that causes the cough. Also at night you are not swallowing you saliva at the same frequency than than during the day giving the acid an easier time to get to your throat. Try sleeping on your left side at an elevated incline, let gravity be your friend.