Fook knows!! I dont think it will be the head unit as its only about a year old and never had any probs with it. As you say it could be loads of things. It does sound like an interference type thump (hence trying the RCA's outside the car) but could be something behind the head unit I suppose. On Alpine units is it the blue/white or the blue that is remote turn on? (the other is the aerial I think).

Chris