This may not be your problem, but here is a funny story that everyone can laugh at me for

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I felt
really stupid when I figured out why my AVR-686 would never properly turn on my PDR-10. I tried increasing the levels in my HTPC for the sub and tried messing with a bunch of different main menu setting options, to no avail.
The individual channel level volume was turned way down, and I never saw it in the menu (my AVR-686 doesn't have an OSD). I finally one day accidentally pressed the enter button on the remote and it brought up the channel select menu, which is independent of the setup menu, where I discovered my sub level was down to -26 dB. This was after
3 years of thinking my sub's auto-on just wasn't sensitive enough. Anyway, now it works like a charm and I don't have to have my sub gain up so high

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My suggestion for your situation would be just as suggested above: to turn the output gain up in the receiver and compensate by turning the gain on the sub itself down, if necessary. You may want to re-run Audyssey afterward too.