According to the Lightroom documentation
Lightroom determines a photo is a duplicate of another file in the catalog if it has the same, original filename; the same Exif capture date and time; and the same file size
Please confirm that your "duplicate" files meet this criterion
Yes, I'm aware of this requirement and as stated in my original post, the file I'm trying to import is an exact copy of the original with the same name and same checksum (which guarantees EXIF data and file size is identical.) Nonetheless, I've also checked these manually.
Can you supply one of these "duplicate" files for others to look at? Use dropbox.com or similar.
Is your problem repeatable for a specific photo, if you make a new catalog and import that one photo into it, then put it somewhere else, and import it, again?