If you are using the server URL for your Joomla installation, you need an appropriate rewrite base added in the .htaccess file in order for SEF URLs to work properly. The .htaccess file should include this line (below the commented out "#RewriteBase /" for a standard Joomla .htaccess file):
RewriteBase /~username/
Where "username" is your actual cPanel username. Note that the RewriteBase should include the full relative path to the Joomla installation. If the installation is placed directly in the public_html directory, you should use:
RewriteBase /~username/ - as specified above
If the Joomla installation is under a sub-directory for public_html, you should use:
RewriteBase /~username/<path to Joomla>/
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