Did you check the Bass setting to make sure it was turned up? I know it might be a silly suggestion, but that may have been easily overlooked, and maybe there was a glitch that put it down to zero for some reason.
Sorry I can't be of any more help. Good luck with the fix!
2001 V8 4.6L Mustang GT (auto) - daily driver
2004 V6 3.9L Mustang (auto) - sold
God bless all!