Are you sure it's thrush? The fact the Daktarin made no difference would make me think it isn't thrush at all.

I don't know if this is the case with you, but my DD damaged my nipple on one side at nearly two and it took months before it was completely healed. It wasn't an ongoing infection or thrush, there were no other symptoms, it was just that her feeding from that side (even only twice a day) was enough to open the wound again every time. I tried pawpaw, which helped, and advanced wound healing bandaids, which also helped, between feeds. I think it was just a size thing for us, the way her teeth rubbed on that spot. It disappeared almost as if by magic, her mouth must have just grown enough to stop irritating the 'crack' (wound).

Taking good care of the damaged nipple in our case definitely stopped it turning into anything worse or getting infected, but it just didn't heal properly for quite a while.

Does that sound anything like what you have?