I'm not sure how inaccessible the port is, since its in your dash. But a good check for whether its lack of signal amplification is to just pop headphones into the port and see what you get.
My guess however is much like your initial thought. A problem with your sound drivers. Though you are clearly very competent to diagnose on your own, I'd also check where it is sending the sound (does it have a digital output that it might be bypassing the analog)
Edit: And I liked the title. I work in a music department- there is always trouble.