I just started listening to the radio again after a long spate of not, and I noticed that there's alternator noise when I'm listening to the tuner, but not when I'm listening to mp3s. (I don't have any Aux hooked up right now.)

Any ideas as to why? I need to open my dash anyway; the tuner module has come loose from its moorings and is rattling around in the dash somewhat anyway. Maybe that has something to do with it?

That's a good guess. Is the tuner grounded internally? Maybe you can give it a known good ground to test.

My understanding is that the tuner's audio if fed digitally into the empeg, so the source of the alternator whine is unlikely to be caused by one of the usual audio ground-loop scenarios.

I'm guessing that the problem is possibly caused by an RF interference mechanism; possibly a bad/loose antenna connection or maybe real alternator whine caused by a faulty suppressor device in the engine bay.

The tuner audio is not digital. That's why there was a problem with earlier versions of the software being unable to do visuals for it.