Another suggestion or two:
I'm assuming that you probably have gone through the auto-set-up process for your receiver (with the microphone, etc.), but if not you should. You probably want to have the sub-woofer's own level control set somewhere around mid-range, so that the auto-set-up has both head-room and "floor-room" to adjust the LFE output appropropriately.
Yamaha's auto-set-up works pretty well, most of the time. But it sometimes sets speaker-size wrong, so that is one thing to double-check using the manual set-up menus. Also, it may get the phase setting of the sub-woofer wrong. This can result in a lot of cancellation of low frequencies, especially if you have your front speakers set to Large. One other thing to try is to manually reverse the phase of the LFE output.