First, thanks for the quick replies! And, after I typed up the reply, this seems to be more of a bottling issue, so the topic may be better suited in the bottling forum, but I don't know how to move the thread.
I use StarSan for everything. On brewday, I sanitize the wort chiller by running star san through it (the wort chiller consists of a counterflow setup, built from copper pipe and garden hose, and a March pump running the wort through the chiller). I sanitize the Glass carboys by racking into them (after a good scrubbing using the carboy brush).
Links posted for information purposes, not endorsing northern brewer (though they have treated me well!)
The bottles were sanitized using about 5 squirts from a vinator gizmo (http://www.northernbrewer.com/brewing/vinator-bottle-rinser.html
) full of the regular star san mix, then letting them drain out. I also wash bottles in the dishwasher as they are used, but they sit in the closet for up to a month or so before reuse. I fill the bottles out of a plastic bucket with a spigot, a length of hose, and standard spring tip bottle filler (http://www.northernbrewer.com/brewing/spring-tip-bottle-filler.html
). Caps sit in a bowl full of sanitizer until they go on the bottles.
Fermentation on this one went a little longer than I normally do, both due to vacation, and some incomplete fermentation I was getting on previous batches. Primary was 11 days, and secondary was about 14. It seemed to taste fine (no sour taste that I recall) before bottling, so I suppose scientific method narrows it down to the bottling regimen.
Thanks for the support!