I have been through two iPhone 3GS's and both have this same call-waiting beep issue. I have also purchased a new Jawbone Prime to replace my Jawbone 2 and both have the same call-waiting beep issue.
The Jawbone 2 did not have the problem with my old Motorola phone, but the replacement iPhone seems to indicate the problem is not unique to a telephone but to the firmware's compatability with the Jawbone.
If, during a call, I unpair the Jawbone, reset the Jawbone, and re-pair the Jawbone, the beep is no longer a problem for the duration of that call. As soon, however, as you make a new call, the beep is back and the three step, cumbersome sequence must be repeated again.
I hope Apple is working on this as it seems to be in their OS.