I also have the RX-a2000 (great avr by the way congrats!!)
Check to see if your mains are set to large & subs to off. because if they are & if the "extra bass" isnt ON then all the LFE will be directed to the mains. Look to see if when you play a movie that the lights on the display show that one of the subs is getting a signal.
Ive found also that if the sub is set to AUTO & if there is not enough low frequency in the programing that it wont trigger the sub to turn on. But since you are getting a tone when YPAO runs means that a signal can at least reach the sub & that the sub should be fine. Its probably something simple. This type of thing happens to me all the time, when i do figure it out it always seems to be something silly.
Hope you get it soon so you can enjoy your new Yammie!!