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Well, you're not missing anything really. More like adding a bunch.
A car environment is completely different from a home PC. You introduce infinitely more interference in an automobile. Also, most of the time your using amplifiers to power your CarPC which introduces a whole lot of issues by itself. The noise, I'm assuming, is coming from your amps being turned on WHILE the computer is booting. Then, as the computer is booting it, and other components, are producing electronic interference during this. Your amps (and/or signal wires) are picking this up and displaying is as audio "noise".
You can check to make sure your not getting a ground loop anywhere. Also, check your RCA's and especially if your using 3.5mm to RCA cables, try moving the 3.5mm plug around a bit. I know that sounds pointless, but in many cases it can quiet down the noises.
After that, your only real option is to have a delay or manually switch to turn on/off the amp(s). In some cases, noise simply can't be eliminated by normal means.
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CarPC:
1.8GHz Northwood, Intel 845 Mobo, 512MB DDR, 1x20GB + 1x160GB, Intel GPU, SB Live 5.1
Sound System:
Phoenix Gold RSD 65cs 6.5" Drivers, Infinity Tweets, Pioneer 305DVC 12", PPI Sedona 630IX, Alpine MRP-M500
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