Thanks, Stefan. I've tried everything I can think of at this point and haven't been able to eliminate it. Swapped HDMI cables. Swapped subwoofer cables. Swapped power cord cables (for both the computer and subwoofer). Removed the paint from the motherboard mounting posts to ensure the posts contact bare metal. Ran a copper wire from the PC chassis to the phono ground pin on the receiver. Updated all drivers. Disabled other onboard devices. Nothing works. But the Roku doesn't have bass noise. So it's definitely an issue between the HTPC and the receiver. I'm just completely stumped by what it is and feeling pretty frustrated.
In the meantime, I can output directly to my TV to avoid the noise problem. Is there any way to fix the error I'm getting with the Intel sound application only giving me options for stereo sound? When I connect to the receiver, I have all the options, from stereo to 7.1, with everything in between. But when I connect to the TV, I only see stereo and Atmos. And trying to enable Atmos results in no sound.