I was using Alpine Type-R components. The speakers still made noise but the sound was absolutely awful. Lots and lots of white noise and scratching mixed in with the music playing faintly in the background. When new they sounded fantastic.

I have the new deck and the SkyFi in the car now. So far I haven't had the same problem. It can make a faint pop (tried it since I'll be replacing the stock speakers anyway) but not nearly as bad as with the old car. Someone on another forum suggested that it was a grounding problem with the SkyFi. Seems OK for now. Fortunately I've learned not to make that mistake in the first place.