requested URL was not found on this server

[eluser]Unknown[/eluser]
Same problem here - fixed with this as the .htaccess file:

RewriteEngine on
RewriteCond $1 !^(index\.php|assets|robots\.txt)
RewriteRule ^(.*)$ index.php/$1 [L]

Instead of this, which is in the CI user guide:

RewriteEngine on
RewriteCond $1 !^(index\.php|images|robots\.txt)
RewriteRule ^(.*)$ /index.php/$1 [L]

Basically, remove the leading "/" before index.php - and if you use an "assets" folder to store your css, images, etc. then add that sucker in there.