My son had thrush when he was 15 months old. The day I went to the pediatrician for it was the night I was planning on weaning him actually, and I never ended up getting it (thankfully). His went away in about two weeks while he was taking Nystatin(?). After it was gone, I continued to sterilize everything for probably another month. My doctor said that yeast is very hardy, meaning it can survive on anything and everything. I even sterilized his toothbrushes daily (I don't know if your son is old enough for those yet) My doctor also said that once you think it is gone, it usually comes back again. A website I saw recommended when you think it's gone, continue to give them the medication for five more days. It doesn't harm them to continue the meds for a little while longer. I gave him the solution like they recommended, but I would also dip a clean, sterile q-tip in the solution and rub it all over his gums.
Here is the website, it has some helpful information:
http://www.askdrsears.com/html/8/T083100.asp
Good luck,
S.
I also wanted to add that I started my son on probiotics also this month. I am thinking since he has had one thrush incident he can be susceptible to more in the future. It also helps with immunity and digestive health. I just bought Culturelle at Target in the Health section. They make one for infants and children.