It's just weird. There was no LFE signal present. It was just normal bass from the program on. But the subs should have kicked on much sooner than -25.
You did say your sub levels were set to -3.5 and -5.5. If you have time do a little experiment described below.
1) You have already set all speakers to small, but now set crossovers of your front, centre and surrounds to 100 Hz, just to make sure there are low frequency signals sent to the subwoofers when playing
non DD and DTS programs.
2) Manually increase the levels of the two subwoofers (in the RX-Z9,
not the subwoofer volume knob) to
0.
3) Set LFE level to -10 again.
4) Now play some CDs or whatever media programs that you know for sure has a lot of bass below 100 Hz but contain
no LFE channel signal; and in Stereo mode to make sure the AVR will use the subwoofer.
5) Start with the AVR master volume at say -25, at where you said it would not wake up the subwoofers.
6) Increase the master volume gradually, say 1 dB at a time and find out at what point the subwoofers will be kick in.
Record every details, then repeat the above steps but with LFE level set back to 0 so you can compare at what master volume the subwoofers kick in.