So I just realized that both the Denon AND my Polk sub are likely going out. I had it running on a different Sony subwoofer before we moved, and it was having the same issue - just not as bad. I had thought it was that sub. Fast forward to now, and the Denon is hooked to the Polk instead of the Sony. Same problem but now worse. Changing the cable didn't help, all settings were correct. I brought a newer Onkyo from another room to replace the Denon, Polk sub is still acting up. Hooked up the Sony sub instead, everything works fine.
Now that I have to get another sub anyway, I'll test that one with the Denon. Hopefully it works. If not, it can make a great donor unit.
Thank you everyone for your advice. It sucks being an amateur at this stuff.