It could be blown (rear) speakers, especially if they are still stock. I had this problem and thought is was my amp. I would check/test the rear speakers with a cheap 2inch speaker you can buy at wal-mart. Take the trunk lining down on the passenger side/Cd Unit and locate/disconnect the +/- connections attach the working speaker to the +/- clips and turn on the radio and prey for sound. Here was my DIY
First half to process:
http://us.lexusownersclub.com/forums/index.php?showtopic=36346&hl=rear+speaker+replacement
Second half: