I'm not aware of research that would indicate that a high protein diet would cause GERD. Fried and fatty meats, citrus products, and high acid foods like tomatoes are the usual suspects. In my case, beer and carbonated products bothered me greatly before GERD surgery.
I had the same problem after high protein diet and nothing seemed to help - prilosec, maalox, gaviscon, etc. I tried everything. In fact these things seems to make symtoms worse. Then a friend suggested I might not have "enough" acid to digest the protein. Hmmm.......well, after a little research, I decided to try a hydrochloric acid supplement and BINGO...........no more acid reflux.
I was a little nervous about taking MORE acid, but decided I could double up on the maalox, etc. It was truly amazing. You might try it to see if it works for you. What can you lose??