This same thing happened to me while I was traveling. I ended up turning off each one of my email accounts one by one to track down which email was causing it to beep every time it checked my mail. It turned out to be my gmail account. I ended up deleted my gmail account, doing a hard reset, and setting my gmail account back up on the iphone.
Seemed to work for me after that. Though every once in a while I'll see that my phone will beep even though I dont have any mail, but its only been once a week or so, and NOT every time it checks my mail like before..
Hopefully you've already fixed this, being a month late to responding to this.