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I am using the incremental backup, to a local filesystem, which is ext4


here is the original files

/home/simon/public_html
-rw-r--r--. 1 simon simon 3.4K Aug 8 00:14 wp-config.php
-rw-r--r--. 1 simon simon 2.7K Apr 13 2015 wp-config-sample.php
drwxr-xr-x. 11 simon simon 4.0K Aug 9 11:27 wp ...

I had the same problem, the software has a problem with permissions

you need to chmod 755 directories, and chmod 644 files, and chown -R owner:owner all the files upon restore