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Yes, what you said makes sense. Specifically, this:

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most of the time, I had the empeg volume nearly as low as it will go

That means your amplifier gains were cranked way way way way way too loud.

Interesting -- because prior to this, I'd already turned them down about half-way from where the installer had them set.

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Setting the amp gains properly is one of the first steps in troubleshooting a whine problem. It's in our installation FAQ as well as in pretty much every other noise troubleshooting guide I've ever seen.

/me goes and re-reads the FAQ.

I hadn't gotten that far before. I didn't actually notice the whine until I noticed that I was only getting audio from one side of the car. I had associated the two, and figured that the whine was a result of, or part of, the same problem, as opposed to realizing that it was actually a completely separate problem altogether. When I found the loose wire, my first thought was "more wires are loose". I think I also had a vague recollection of reading this portion of the ground-loop FAQ:

For instance, the common term "alternator whine" makes it sound like the problem is the alternator, but usually the real source of the problem is a ground loop.

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Also, based on this statement:
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and turning the empeg up a bit closer to 0dB (well, it's now just past the middle, so that I still have some room to go up, if needed)

At that point you could still stand to have the amp gains set even farther down. The ideal, best quality signal will be had when you are able to turn the empeg all the way up to 0db and that is exactly the loudest you would ever want to play the stereo when you're at 80mph on the freeway.

I actually have it so that it's the loudest I'd want to play the stereo when I'm loading and unloading stuff from the bed of the truck, which is quite a bit louder than when I'm going 80mph on a freeway. (Though they could still use a bit more adjustment further down, yes.)

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The problem seems "fixed", but is it really just "masked"?

No, it's actually fixed. Like I said, all systems have a noise floor. You were just cranking up the noise floor.

Cool. Now I have the terminology to match my reasoning.

Thanks for a very clear answer, and an FAQ that makes sense (especially now that I've actually had a real-life lesson in it.)