I don't think there's much difference. I think the expressions could be used interchangeably -- even within the same paragraph -- without drawing any attention.
I think there is a slight preference to use "made FROM" when the original material is largely unchanged:
> The desk in the Oval Office was made from the timbers of the USS Champion.
> Our applesauce is made from fresh-picked apples grown in our own orchards.
> She made a book bag from a skirt that no longer fit.
Possibly the expression "made OF" is preferred when the original material has been vastly altered:
> Plastic bottles are made of long-chain organic molecules.
> Happiness is made of many factors.
"Made OUT of" may possibly be used to emphasize the fashioning process itself, rather than the nature of the materials, so it is perhaps used in both the case where the original material has been greatly altered as well as the case where it is largely unchanged:
> Debrett makes his artwork out of items he finds by the side of the road.
> I made this poetry out of my experiences in the war.
But really there is almost no difference. I doubt anyone would ever notice the minuscule differences here:
> Watermelon sherbet is made from watermelons and sugar.
> Watermelon sherbet is made of watermelons and sugar.
> Watermelon sherbet is made out of watermelons and sugar.