i'll take a crack at this..........
1) is your computer in the trunk with the pwrsupply? i ask this because when you run your RCA cables from the back of the car to the front headunit under the carpet, some people just put all the wires in a loom with the pwr wire. This causes some interferance with the RCA cables. Make sure you run your pwr wire on one side of the car and the speaker wires on the other side.
2) I take it that without the computer setup connected you don't have the wine and the stereo was working okay?
3) Have you checked ALL your RCA connections? the reason i ask is because i made my own and with one of them i soldered the connector on sloppy and it was causing a wine only when the car was running.
Hope this might help.