When in "bypass" mode and analog inpout, what really counts is the toggle on the back of the unit. Make sure it's in "bypass" position (the middle position) as well.
If it's in LPF/HPF it will engage the passive analog crossover and frequencies below 80Hz will go to your sub.
The manual makes you believe the toggle on the back applies only to 7.1 bypass mode, but in fact it applies to everything analog in bypass mode, including the tuner.
That toggle on the back of the unit is the equivalent of "analog bass management", if you want, the signal doesn't go through A/D/A phases as DSP circuit is bypassed while still allowing listeners with small speakers and sub use the unit in stereo bypass mode.