Check fuse number 7 (20A) in the under-dash fuse box. Don't go by appearance, use a multimeter to test it or replace it with a good 20A fuse. Fuse box diagram here (2003-2006) : http://www.skidmore.edu/~pdwyer/e/udfrb.htm
my radio/amp (element 2003) has a similar problem: when disconnected from the battery and reconnected again, everything works fine but NO SOUND! whatever. After a long search I found out that disconnecting and connecting again was the solution, sound came back. It seems like there is a switch somewhere which toggles by disconnecting from the mains. Nobody could explain it, but it still works that way: after a flat battery I have to disconnected once more to get my sound back. Maybe this helps?