If it's on all sources. It might be the internal amp going bad in the headunit. Do you have the shaker system. If so does it do it just in 6x8 speakers. Or in the 8 in the door. Because the only thing the amp powers is the subs in the door for the 500 system.
If the amp is bad for the subs you would have to replace it with a factory one. Or you could possibly change to an aftermarket one and wire into the factory subs. Which can be a pain. But I would check the RCA outputs on your headunit and make sure they are ok. They can go bad.
Ever figure this out, mine has done this on occasion. If I take my left foot and tap it against the amps on the drivers side the sound thuds through the speakers when I thud against the amps. Bad ground???