I flew CO TPA-IAH-SMF last week, and had this problem using my Shure noise isolation headphones, but I was able to solve it. On a Delta flight a few weeks ago, I was listening to music on the AVOD screens on a 757 Transcon, and with the high-quality headphones, I couldn't turn the volume down low enough to not be too loud. So I went to Radio Shack and bought a volume control device (just $5) that I can connect to my headphones. It works like a charm and is very small and light.

So on the CO 737-900, I just turned the plane's volume all the way up to where the beeping was non-existent or barely noticeable, then turned the volume down with my new volume control. Problem solved.

-Michael