It seems like WP multisite installation? In that case, you’ll need to manually add HMWP rules in your site’s .htaccess file.
Please, follow the video tutorial here – http://support.wpwave.com/videos/multisite-setup
Regarding logo not being displayed, please try adding following replacement in “Replace in HTML” option under Replace Tools tab:
"file/ ==> "/file/
If it’s still the issue then please let us know your site’s wp-admin login details and FTP details as private reply so that we can look into it further.
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This reply was modified 7 years, 5 months ago by
Suman M..