What's your procedure for chilling your wort down to pitching temp? I know that if you let it sit for too long, it can pick up some nasty stuff. I've outlined one of my favorite tricks when doing extract with the bottled water below.
On brew day, pick up 6 gallons of artesian water (not distilled, that takes out too much of the good stuff in the water). Put 3 gallons in the freezer when you start brewing (or, if you can plan ahead, put 3 gallons in the fridge the night before). Don't let the water freeze though. Then, make your wort as you normally would. After you've finished your boil, you should have about 2 gallons left. Add the 3 cold gallons of bottled water to your wort, take a temp reading, and pitch when you're at your target temp.