Some have had longstanding problems with whine (for instance, see edsmiata's thread "I give up!!!")
In those cases, I'm reasonably certain that the problem isn't with the empeg itself. Those who have solved their problems have always come back and said "Oh, it turns out I used a crappy ground point", or "Oh, my amp was a piece of crap, I replaced it with a better one and the problem is gone," etc. Either that, or it's a malfunction in the empeg such as a loose wire or solder joint. I'm sure edsmiata is something similar, because when he pushes on the on the player the whine goes away.
My answer was referring to the empeg design in general. In other words, I'm saying the Mk2 units aren't any more whine-prone than any other stereo with a separate amp. I'm not saying people haven't had trouble, I'm saying that they haven't had any more instances of trouble than you would expect from a separate-amp installation of any other car stereo.
The Mk1 units are a different story, of course.