When PHP and FTP run as different users and you've uploaded some files via FTP, you can end up in a scenario where WSN is unable to write files and thus generates errors. Ideally, you would fix the server setup to run PHP and FTP as the same user. If that's not possible then install with the autosetup.php after CHMODing the site to 777, and then avoid ever manually replacing files. However, as a backup in case these options aren't possible for you, you can give WSN your FTP info so that WSN can fix file permissions problems when it runs into them. Supply your FTP info at Admin Panel -> Settings -> System Configuration. Warning: If your FTP info changes (such as when you switch web hosts or have to change a password after a security breach), be sure to update the info on the system configuration page.

FTP Host: typically ftp.yourdomain.com
FTP User: yourname
FTP Password: the password for the user
FTP Directory: the path you follow to reach your WSN install from where FTP drops you. Do not include a trailing slash. Typical example: public_html/directory

Note that some servers don't have PHP's FTP extension loaded, and so cannot use this feature. In such a case, the FTP options simply won't appear on the page. The FTP options also will not appear if PHP and FTP are running as the same user, because it's not needed in that case.