As you say I think Windows files and your software as mangled up when it's loaded. Have you checked Control Panel? Have a poke around the sound icons in there. You may find something that is the Problem. Also it may be worth a look in Device Manager to make sure the drivers have loaded correctly
As you have treble and bass settings on the speakers and these are the actual source of the sound that you hear, any graphic equaliser(s) settings should be left flat; use the speakers' treble and bass controls to tailor the final sound output.