I have never heard the sound you describe on our Twins. Make sure it isn't something in the room! Also it could be something with that much very sustained low end is just too much for something inside the box. Try with a sub and see if it subsides (pun intended).

As far as your +3 setting goes, my guess would be your room first. But then again, if you are listening to the LF sound you described for prolonged periods of time it could be your hearing!