I remember having this issue when using the stock port for the short period of time before replacing the stock HU. This has not been an issue since using the Pioneer HU with the two rear USB ports. I am using the Apple USB charger chord in one port to charge and play audio on my phone and the USB to USB chord that came with the Pioneer with a flash drive connected to it in the glove in the other port. Sorry if that was no help for your situation.
my last cable i used for the aux port introduced engine rev noise inbetween songs. the cord before didnt have that issue but it did cost $25 compared to the $10 version that did whine. now that i went to a ibolt mount for my sgs3, the noise went away again.