The most likely cause for this, is that Google somehow flags the files as not belonging to Duplicati.
If you use the Google Drive (limited) option when creating the AuthID, Duplicati will only be able to read files it has created itself. If you somehow touch the files, Google will mark them as no longer belonging to Duplicati, and AFAIK you cannot change that back. The only workaround I know of, is to re-upload the files with the limited auth-id, which will mark them correctly again.
The Duplicat.CommandLine.BackendTool.exe is usually found in /usr/lib/Duplicati on Linux.
You can use the Google Drive (full access) option when creating the AuthID, which will give Duplicati full access to all files in the account, altough I recommend not using that option as it violates the “least-privileges” precaution.