Late better than never?
I'm a new user and noticed this wasn't resolved when looking for something similar.
But I've had this experience and for those searching on it later, I thought I'd still mention it here.
My experience was that my car did that as well when the volume on the device that is connected to the aux in port is too high. That doesn't mean that the volume actually *is* too high, it's just that the signal coming in is too high so if you turn the volume down a little on the device and then use the volume on your stereo to turn up the volume, the popping and cracking goes away.
As with all things, your mileage may vary.
Cheers!