Speakers cut out when truck is cold

[mick14]

I have an aftermarket stereo hooked to my stock Navigation with lockpick and am having a problem with passenger side speakers cutting out and having engine whine when truck is cold. Weird thing is, it is only with media hooked to sync. If my phone or ipod are playing music through blue tooth or usb cable i have this problem. If i switch to jukebox, radio or satellite it goes away. Go back to to usb or bluetooth and it is there again. After the truck warms up it is gone. Any ideas? It wasn't there when stereo was first installed but has now shown up. Worried that the dealer will blame it on stereo even though nothing aftermarket was directly tied to sync? Any ideas?