Yeah the Nystatin contains sugar, and since yeast thrives on sugar and its becoming resistant to the nystatin, it just won't work.
www.kellymom.com has great info on using gentian violet and on thrush in general. Here is what I did both times we got thrush, and it was cleared up in a matter of days.
Get the gentian violet, and dip a q-tip in, then paint your babies mouth with it, top, bottom, gums, tongue, everything until his whole mouth is purple. Then do the same to both of your nipples, but never re-dip the q-tip, use an ew one for each nipple and for his mouth soas not to contaminate the bottle or a part thats doesn't already ahve thrush.
THEN go get the acidophilus caplets you can break open, and put a bit of the powder on yoru finger and put it in his mouth, and you start taking two caplets three times a day. Acidophilus is a probiotic, which will fight the thrush, a bad bacteria, out of your body. Then when the thrush is gone, just slowly 'wean' your self off it, drop to one caplet twice a day, then one caplet a day, and the nstop if you want. You can give your baby just a bit on your finger once or twice a day, but he will get hte probiotics through your milk as well, but at first I'd give him a bit on your finger or on his tongue to fight it off quicker.
It should only take one application of hte gentian violet to get rid of the thrush, and the acidophlus I'd continue taking for a couple weeks. but check otu kellymom.com for more great info.