The primary differences I see is in this section:
Code:
# Uncomment following line if your webserver's URL
# is not directly related to physical file paths.
# Update Your Joomla! Directory (just / for root)
# RewriteBase /
########## Begin - Joomla! core SEF Section
#
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} !^/index.php
RewriteCond %{REQUEST_URI} (/|\.php|\.html|\.htm|\.feed|\.pdf|\.raw|/[^.]*)$ [NC]
RewriteRule (.*) index.php
RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization},L]
#
########## End - Joomla! core SEF Section
I believe you can comment out the RewriteBase line since the server does use physical file paths. Also there might be something in the RewriteCond and RewriteRule statments that might make a difference. The only difference between my installation and yours is that you have installed it in a sub-directory, but assuming your .htaccess file is in the sub-directory that joomla is in, it shouldn't make a difference.