I renamed some photos and FTP copied them to a different folder only to be surprised that some of them ,(about 5%), had new entries in the tag_to_obj table automatically populated by opening up the front end of the browser to the site. While I know that zenphoto would add entries to the images table when I added those photos, I'm confused as to how it knew to correctly attribute some of them for tags. Can anyone shed light on this? The new file names resembled the old ones but were different.

Those images probably had keywords in their metadata. Zenphoto does extract metadata from images that matches its metadata.