I have had similar issues with my 2013 Sync in my xlt.
I am running the same ipod and wire as I did in my 2010 and it is horrible.
The new truck indexes every single time I turn the truck on and also says speech commands not available for this device. What a crock. I can be listening to my ipod. Stop put gas in the truck jump back in, and it will index, and then say speech commands not available, when 15 minutes earlier, I was giving it speech commands.
Does anyone test this stuff. It is ridiculous. They always tell me its the ipods fault. When I remove the ipod, it is working find and it paused right where I shut the truck off waiting for a command, so its not the ipod. Very Frustrating in a new truck.
Where was the fuse box that you pulled the fuse on? Under hood, or somewhere else?
Thanks for posting this.