What can happen (not sure that it is what is happening here), is that if you have a happy little colony of both thrush and bacteria then killing one of them allows the other one to breed madly - and can make things worse. So sometimes antifungals can allow the bacteria to go bananas.
Stupid question - but if you do think you have an infection of some sort, are you washing bras and breastpads in hottish water and rinsing them very well? I know that for me it is washing powder residue that gives me nipple-eczema, so I only put a quarter of the recommended amount in to the wash.....