This story has some elements of urban myth in it - see http://www.snopes.com/critters/crusader/stuffedtoys.asp
As they point out its not only stuffed toys that are treated with anti fungals/bacterials - fillings of duvets/doonas/quilts/comforters/ pillows/cushions/pet beds are all potentially treated with the same chemicals.
Also there is no details that if you wash toy/quilt whether the chemical is removed/reduced.
I would also be very surprised if there were any standards imposed on what is deemed appropriate or safe for pet toys - there seems to be little or no regulation as to what can be fed/added to pet food around the world.
That is not to say that there are very good manufacturers of pet food/toys who take the research upon themselves. However if I went along to my local craft store and bought a commercially available filling, how would I know whether it had been treated or not?
We used to have Blue Jays come around and really squawk and squawk. Now we have crows, mostly mornings doing the squawking, squirrels doing the whining and a woodpecker playing the drums on the telephone poles. Natures band!
