we have 6 trucks like this. Two of them have had to have a junction box (up inside the dash, not the fusebox) replaced. they exhibited the same symptoms as your own.
wish I could give you an easy answer, but thats the best I have right now! good luck!
My 2005 F350 does the same thing. In the morning the radio and windows usually doesnt work for 30 seconds to 5 minutes except when at the dealer. All fuses, breakers and relays are working properly. It really sucks.