Good idea.
To help troubleshoot this, you're going to want to check if it's a cable, the source signal, the receiver, or the sub that are causing this issue. You seem confident that it's neither the sub cable or the sub causing this, so let's focus on the others.
Here are some ideas to start with:
1. Try swapping the cables that connect your computer to your receiver. I'm assuming that you're using cables with a stereo 3.5mm jack on one end and dual RCA jacks on the other (one cable for front L/R, and one cable for center/sub). Switch those around, both where you have them connected on the computer and where you have them connected on the receiver. If both front speakers and the center speaker still work, then it's not the cables.
2. Check out page 88 of your Onkyo owner's manual (which, if I got the model correct, is linked
here). It describes setting the subwoofer sensitivity for that analog subwoofer input. The default should be the loudest setting, but that setting might have gotten adjusted at some point in the past and is now causing you to not hear the sub (you can adjust it to be reduced by 15dB).