It’s found via a database query, but how it got that way isn’t clear. Presumably a filesystem walk did that.
Can you see any similar sort of repetition using the tree command, perhaps with output piped to findstr?
Is the freenas home directory unique to this user, or do other users have them too (except working fine)? Regardless, narrowing down the scope of the problem using a special partial test backup may be useful.
Was this determined on freenas or Windows? Checking may be difficult. Bind mounts may also factor in. Regarding symlinks (if that is still remotely a possible situation), Windows has interpretation settings like:
C:\>fsutil behavior query symlinkEvaluation
Local to local symbolic links are enabled.
Local to remote symbolic links are enabled.
Remote to local symbolic links are disabled.
Remote to remote symbolic links are disabled.
although from what I’ve read (and I’m not set up to test), issues in this area would be different than yours.
Another way to see what Duplicati is doing is to set up –log-file with –log-file-log-level=Verbose, which will show Duplicati’s filesystem traversal, possibly giving some clues as to why folders show up repeatedly…
glogg might be a good way to sift through a large log. Or narrow the scope down first, and get smaller log.