Sorry, I'd missed that part before.
No trouble. I don't mind repeating myself when other people are spending their time to help me out.

That's very VERY interesting that the line-out plugs are fine but the docking connector is bad. This means that the hardware fault is very limited. Maybe something as simple as a dirty or loose contact on the docking sled connector. Maybe you don't need to send this to Stu after all.
That's what I was thinking. There must be something that's splitting that signal, sending some to the RCA connectors, sending some to the dock pins. If that "something" is gone/going wrong, then everything's just going to the RCA connectors.
Are you using four channels, or two, from the docking connector?
I'm using four channels, but it doesn't matter, because...
Is it both the front and rear outputs on the docking connector that have this problem, or just the rear?
...it's both.
I'll double check, though I'm not convinced this is where the problem lays.
What sort of voltage readings should I be getting for these pins? That might help narrow things down... if I pull the docking connectors off the headers on the mobo, I can measure voltage levels coming directly off the mobo pins. If they're fine there, then I'll know the problem lies in the dock connector wiring somewhere.