My first questions would be: What are you running through the chiller? Is it just water from the backyard hose? And: are you sure the chiller isn't leaking into the wort?
Otherwise, I can't see how it can be causing the infections.
Capt. Pushy, BN Army Corps of Engineers
(not to be confused with Push E.)
I am just running cold water from the hose. I haven't checked in depth for leaks which I will do today. I'm actually at home this week and will have the opportunity to brew.
Are your fittings / ends of your chiller hanging out of the brew pot - in other words, they may not get sterilised by putting the rest of your chiller into boiling wort and moisture (bacterially loaded) may drip back in to sufficiently cooled wort.