The backup destination is completely irrelevant to the backup code that reads the files, so the only explanation I can think of is that they are running in different processes, or that something else (anti virus?) is accessing the files at the same time.
The exception is specifically UnauthorizedAccessException which should precisely mean that the current user (that which is running Duplicati) does not have access to the file. Seeing that Duplicati can enumerate the folder (to get the file name) it must be a permission on the file. Can you check that the permissions look plain?
The logic is that it is common enough that there are “flukes” were something prevents reading a file. Most such errors are transient, so they are treated as warnings.
We don’t currently have any classification of errors (permissions, file locked, I/O error, etc), so we consider all errors to be transient, which is not always true.
It would like to handle this a little better, and have created an issue for this.