Your manual says:
DIRECT – Sources are heard according to the settings made in the Surround Setup (speaker setting, channel level, speaker distance, acoustic calibration EQ, and X-curve), as well as with dual mono, the input attenuator, and any sound delay and hi-bit/hi-sampling (SC-25 only) settings. You will hear sources according to the number of channels in the signal.
PURE DIRECT – Analog sources are heard without any digital processing.
To me, this is pretty clear PURE DIRECT won't use your subs.
Even DIRECT won't use the subs unless there is a .1 LFE signal present, (which means not in music). But I'm not sure what they mean by "speaker setting" or "acoustic calibration EQ). Best to look at your panel display and see if the sub is turned on.