A few days ago I was listening to a CD and the subwoofer stopped working in between tracks. I drove the truck for 3 days with no sub and then this morning when I get in for work it's working again.

Has anyone else encountered this problem?

Also, when it wasn't working the sub would make some nasty crackling noises when I turned the igniton key on and off and when the auto headlamps went on or off.

 

Sounds like a short.
The next time it goes out, have the dealership check the wiring.