Gday mate,
Me and a mate had a heap of interference issues with the stereo setup in his vl. It doesn't sound like the same issue, but it could be the same fix. Worth a shot.
He had an issue which was called "ground loop". I can't really explain as I don't understand the issue really well. Basically what we did was use a noise suppressor on the RCA cables to the amp. You may have a really small, hard to find and recitfy noise problem, wither through the alternator or the aerial or something, which is producing noise in the RCA's.
Jaycar sells the suppressors and they r fairly cheap, so give that a shot, might be an easy fix.
Hope you get it sorted out, sounds like a damn annoying issue. From what i can remember, ground loop was an issue with slightly warn components, and even some brand new gear, leaking a very small voltage through the ground, which then goes in the ground of other components. Don't quote me on this, as I'm not sure about it at all, and to me it sounds like BS, but if you google ground loop, you'll get an explanation of it.
That'd be where i'd look.
cheers,
-smurf