First....
"yeah, the subwoofer always has been hooked up through the pre outs on the denon."
Do you really mean "pre outs", as in the receivers preamp outputs, or are you referring to the actual subwoofer output? You should be using the subwoofer output.....just want to be sure.
Now.....
"Go into system setup menu on your Denon, go into channel level setup, set test tone to manual, move down to test tone start and push left arrow to start test tone. A screen will come up with all your speakers and subwoofer on it. Move arrow down to SW"......and adjust the subwoofer output level. "What happens when you adjust the output level to the subwoofer? Is there a noticable change in the output."
Try this and let us know what happens.