Not sure if this is what you are hearing or not, but to offer some input...
You will hear the typical turbo whistle when using the exhaust brake, because the turbo is actually spooling up and building pressure.
Mine blows 5-10lbs of pressure with the brake activated depending on engine RPM, the whistle sounds the same as when I'm under power.
Naturally that sound will always be there, but could be something you may not have noticed before.
Only the 6. 7 reacts this way, the 5. 9 with exhaust brakes would not spool the turbo up enough to build pressure. Since the 6. 7 brake is actually closing the veins within the turbo, it naturally spools up as it does it, in turn making it even more effective.