I'm almost positive now the filter does not apply to a themed site using the same navigation on each page. I've found, at least for my site, the filter was trigged when someone copied part of a page of mine in answer to a question on a forum
I've put a noindex tag on all the articles I've written that have been copied in forums or fully on a web page by others. It's kind of pathetic when the author of articles has to noindex them or take them down in these circumstances. But I don't want to take the chance of a dupe penalty like my small site had temporarily during Bourbon. Even though it got corrected it may not next time.