I don't know if it matters, but I should probably mention; I don't use an iPod, I'm using a flash drive. (this one, btw, http://www.sandisk.com/products/usb/drives/cruzer-fit/
....which I can't recommend highly enough. It stick out of the USB plug less than a 1/4", about the same as the power outlet cover that is above the USB plug. Pictures of it in my center console available upon request.).
Anyway, I have never had to unplug it, and then plug it back in to get MyLink to recognize it. I leave it plugged in all the time (unless of course, I remove it to add more music). The music is always there.
My solution of powering off the radio before shutting off the car just gets the same source to come back on when starting the car the next time, as opposed to MyLink reverting back to FM upon restart.