Subdirectories being flagged despite exclusion

I have the same problem reported (and supposedly resolved) here. I have excluded directories in the “Exclude all files in these directories” box, yet files in subdirectories of those excluded directories are being flagged.

For example, I’ve excluded
/home/customer/www/domain.com/public_html/excluded/, but files in /home/customer/www/domain.com/public_html/excluded/subdir/ are being flagged.