If you've installed a graphics card which has integrated audio chip (most do nowadays), and you've installed audio drivers along with GPU drivers from the Geforce or AMD driver package, that's what's causing the problem as it is now the default audio device instead of the device which outputs through the 3.5mm audio jack. USB headphones still work because they incorporate their own sound-chip in the headphone housing.
What I did was uninstall the graphics driver package completely, then re-installed using the custom-install option, making sure to deselect the audio drivers. This restored the motherboard's integrated audio as the default.