Good diagnostics.
Possible bad component or loose solder pad on the motherboard somewhere, Might be time to talk to Stu.
Wild random guess at something, though... Try switching to a different equalizer preset and see if that fixes it. If so, then it just means a corrupted EQ setting that needs to be rewritten.
I've never touched the EQ settings -- they've always been flat. I've fiddled with the balance settings, and have gone from all-the-way left to all-the-way right, with the expected outcome when you don't have any left audio. It's currently set to dead center. (Hah... I must have had it set on dead left at some point!)
If anyone can chime with a set of components to check (have multimeter, but no logic analyzers, or anything else like that), and/or areas to check for loose solder connections, I can do that when I get home (provided that it's simple enough). If someone can say "oh, yeah... you need to replace XYZ component," I might be able to convince one of the hardware gurus here at work to help out with that.