BackWPup version 3.1.3 Archive

I have been using previous versions for BackWPup to a Zip Archive, transferred to Dropbox without problem.

With the upgrade to the latest version 3.1.3 of BackWPup, now getting the error:-

[16-Nov-2014 12:05:50] 1. Trying to create backup archive …
[16-Nov-2014 12:05:50] Compressing files as ZipArchive. Please be patient, this may take a moment.
[16-Nov-2014 12:05:50] ERROR: ZipArchive returns status: Entry has been deleted
[16-Nov-2014 12:05:55] Backup archive created.
[16-Nov-2014 12:05:55] Archive size is 21.02 MB.
[16-Nov-2014 12:05:55] 3645 Files with 48.18 MB in Archive.

In spite of this, the archive does appear to be created with the right files in it, but the process is recorded as an error and sends the error email.

I see that this has also happened with previous versions and one recommendation is to go to tar.gz archives. I have done this, and don’t get the errors any more, but I get duplicates of the following 2 files within the archive:-

backwpup_readme.txt (different dates, same size 512 bytes)
manifest.json (different dates and sizes)

I don’t know if any other files are duplicated in the archive.

There is only one copy of the above files on the site.

The site being backed up is small – the tar.gz file is 21MB (the ZIP file is 17MB) and it performs the backup in about 30 seconds (whichever archive type is selected), so this is not a script timeout.