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.

Remember that all audio systems have a noise floor. By cranking up the amplifiers so high, you were simply amplifying that noise floor. All you've done is adjusted things properly for once. Poof, magic, now it sounds right.

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.

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.

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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.
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Tony Fabris