I sometimes get the same problem. I contacted empeg and they said it was probably to do with a negative spike when I shutdown or startup. They sent me a new connector that incorporates a diode to stop this problem. I haven't installed it yet (gonna do it when I put my tuner in) but I know how to start my car so that it happens less. Try contacting the boys at empeg.

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Steve - 18GB Mk II Amber
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Steve

2x80GB Mk II with Illuminated buttons