If you have aspirated some of the gastric contents from your stomach into your lungs, you will have a cough...for a while. Gastric secretions don't belong in your lungs and your body is trying still to cough it up. I believe the Pantecta is to treat the reflux. Have you tried any of the OTC cough meds? They might help you out.
I have GERD and do have it so badly that I sometimes aspirate like you. I've had aspiration pneumonitis several times...not fun, and have coughed so much that I injured my back doing so. Now that you know what the cause, you might get your MD to give you something for the cough to get you over the hump.
I am not familiar with Pantecta, but there are a lot of life style changes that are VERY effective.
1) Raise the head of your bed at least 6 inches or get a wedge pillow and learn to sleep on it.
2) Avoid caffeine and chocolate.
3) Avoid spicey foods.
4) Do not eat or drink anything within 4 hours of going to bed.
I have a friend that swears by pure carrot juice, although it didn't work for me.
Also, if you have take antibiotics much in your lifetime, you might want to try a good pro-biotic. My husband makes fun of me, but I will NEVER be without my pro-biotic again. I ran our a while back and didn't get more for about a week. I was MISERABLE!! I also take a digestive enzyme and find those quite helpful as well.
Actually I am pro-biotics at the moment and a good friend told me about food enzyme, which I am going to get at the pharmacy today.. Thanks for all the info , very much appreciate it..