Please clarify what you're actually doing - setting speaker volumes using the Yamaha test tones? If so, I have a vague thought from when I used to have a Yamaha AVR that the test tone didn't go to the sub. Do you have a DVD with THX Optimiser on it? That will work assuming you have the Yamaha settings correct.
To be honest, I've never found test tones particularly helpful for subs. IME better to set by ear using a movie passage that you're familiar with.
Sources: NAD S-500i CDP; Oppo BDP-83SE Special Edition Bluray; MySky+ HDi
Amplifiers: NAD M15 HD2 AV Surround Sound Preamplifier; NAD M25 7 Channel Power Amplifier
Speakers: Proac D25; Proac CC2; Proac Studio 125; REL Storm 5
Display: Panasonic TH-P54V20Z Plasma
Cabling: Wireworld; Nordost
Accessories: Sound Organisation rack; Sound Creations rack; Polycrystal cones