R.M.
My first guess is that you are not using the nystatin or gentian violet long enough. Even when the thrush has cleared up, to the naked eye, it is still there. Try one of the remedies again and continue to use it for 3 days after you can no longer see any visual evidence of the thrush.
Also, try to limit how long he is keeping a bottle in his mouth when he is not actually drinking. This just increase the possibility of reinfection. I would also be tempted to throw out all of his pacifiers and start over again, there are just too many little crevices where the bacteria can hid in those!!