If I'm not mistaken, at least some of the NEO6 (etc.) options won't provide anything via the subwoofer.
<scratching my head if that's not it, considering what else you've tried...>
You might also try asking @ avsforum.com.
I got an Onkyo SKS-HT540 7.1 speaker system setup to a Sony STR-DH520 reciever. My sub-woofer is connected and receiving a signal just fine, even enters stand-by mode when there isn't a signal and turns on when an "LFE" signal is present, but no sound of any kind is produced at anytime. Not even a test-tone. I've turned the cross-over all the way up and set my speakers to "small", but still get nothing from the sub. I've reset my receiver to factory settings, in case it was some custom set-up that was causing the problem, but I still get nothing. My speaker specs as read from the manual are...
Subwoofer - Frequency response 25 Hz-150 Hz
Front & Center Speakers - Frequency response 55 Hz-50 kHz / Crossover Frequency 4.5 kHz
Surround Speakers - Frequency response 60 Hz-20 kHz / Crossover Frequency 10 kHz
Though my receiver has the the Crossover Frequency for all the speakers set at 120 Hz.