Shame after all this time you haven't got to the bottom of your running issues. It has to be software related, I'm sure an update will cure it if one is released.
I've got a £2.5k sound system in my Mondeo lol, all run through the factory head unit. I use a JL cleansweep signal processor which is a great bit of kit, have a look into audison units as they are raved about. I have fully sound deadened mine, makes a big difference.