Yes, old thread but I am going to bring it up. Very frustrating the OP never posted the solution. This is a somewhat common problem, yet after finding dozens of threads on the issue not one OP ever posted the fix. I am having this issue on my 2005 Bonneville SLE and am going to be focused on loose, broken wires, specifically in the harness between the cab and the drivers door. The harness is brutal to exam.

I am not looking at a water under the carpet issue, as when the radio stays on with the car off after exiting the vehicle is not typically a water under the carpet issue.

Just finished the troubleshooting and repair. It was the 12v supply to the driver door module was split in half inside the harness between the door and the body. Did not measure 12v at the small orange wire at the driver door module, did see 12 v at the door module fuse, so cut the harness protector with a razor blade and there was an open orange wire. Measure 12v at one side of the open, nothing at the other. Put in a alligator clip and everything worked, so put in a wire jumper, soldered the ends, electric tape, and put it all back together. Also notice the thick orange wire which provided 12v to the window actuators had a cut in the insulation, so I put some tape to reduce further damage.

Spent a day on-line trying to identify the issue. Fairly common issue, yet almost nobody ever posted the solution.