FWIW, I've switched to sanitizing all of my bottles with Star San before filling (and thus probably have a lot more in the finished product than you) and have not noticed any soapy or off flavors since the switch. That being said, I don't brew lagers (ciders and ales), so if it's as faint as you're suggesting, it may just be going unnoticed. I say make up some Star San and smell it and see if it has a soapy aroma. While I've never noticed any, I try not to sniff my chemicals.
EDIT: I should add that my last batch I messed up and accidentally dumped about a quart of Star San into my fermenter and it still tasted great.
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