The option "Exclude Mac resource forks" does not actually do what it implies. According to the changelog:
Added an option to exclude hidden files (Mac Forks)
Hidden files are not resource forks. Hidden files are just files that are typically not visible to the end user, either due to naming (ie, starting with a period like .DS_Store) or do to having the "hidden" property set.
In fact, the referenced issue 2913035 (http://sourceforge.net/tracker/?func=detail&aid=2913035&group_id=275361&atid=1169898) is pretty clear in it's request, which is to have an option to not include hidden files. I'd add the request that there be a way to edit the list of hidden match strings (a simple text edit field perhaps).
Anyway, please rename this option to something like "Exclude hidden system files" (and, if the list is editable, with a "Edit Exclusion List…" button to the right).