I have no idea what causes this problem, sorry.

Are you willing to 'test' if the home line-out and serial-on-empeg are working when the player is docked (assuming of course you're supplying power through the docking-connector.) For the USB connection it may be needed to start the player with the -u option? I can't try these things myself right now, since my car isn't here. Could check tomorrow, but you having a box right in front of you makes 'the test' easier, since I still have to take out the sled anyway. Mucho gracias!