OK danzcool, I'll try that. However, I've gotten conflicting instructions concerning where that fuse is located. The manual says its on the passenger side, under glove box but I've also been told its under the hood. Can you point me in the right direction? I'm not too car-savvy, can you tell?

 

There are 2 locations that fuses are located, as you noted the passenger footwell side panel (smart junction box) and under the hood (also passenger side between battery and washer fluid reservoir) this is called the BEC, this tends to be more high powered items.
The following links to a diagram of the electrical for the audio system.
http://iihs.net/fsm/?d=40&f=Audio%20...Navigation.pdf

It's difficult to read and you'll likely need to find a map of the fuse boxes, but in the engine compartment fuse 56 supplies power to the audio system, in the smart junction box (passenger side kick panel) fuses 6 & 20 also provide power to the audio system.
It appears only the fuse under the hood supplies power at all times (probably to maintain the clock & presets), so I would start there since it is the only power that should be active when the car is shut off and locked, so try fuse 56 first.

 

I try to disconnect the aux jack, and it works just like magic. Thanks you so much danzcool.

 

No problem, that's why I post whatever solution I found out that I could not find elsewhere.

 

Hi, what i did on my 2007 GT/CS i unplug the aux. cable connected inside the armrest all of a sudden my remote key works just like magic. So if you have connected Auxiliary cable try it my friend nothing to lose on trying. We have the same actual issue. Good luck.

 

you have helped me a few times since I bought my mustang a month ago! I literally just joined this forum because of you LOL thank you so much