Rewrite works differently on Linux than Windows?

So I used to use windows for my apache server, but I decided to move to linux recently.

I had been using the following in my vhosts file, rather than adding a new entry for each site...

<VirtualHost *:80>
        ServerAdmin webmaster@localhost

        DocumentRoot /var/www
        RewriteEngine On
        #www.domain.tld
                RewriteCond %{HTTP_HOST} ^www\.([^.]+)\.([^.]+)
                RewriteCond %{REQUEST_FILENAME} !-f
                RewriteCond %{REQUEST_FILENAME} !-d
                RewriteRule ^(.*)%$ /%1.%2/$1 [L]
        #end www.domain.tld
        #subdomain.domain.tld
                RewriteCond %{HTTP_HOST} ^([^.]+)\.([^.]+)\.([^.]+)
                RewriteCond %{REQUEST_FILENAME} !-f
                RewriteCond %{REQUEST_FILENAME} !-d
                RewriteRule ^(.*)$ /%1.%2.%3/$1 [L]
        #end subdomain.domain.tld
        #domain.tld
                RewriteCond %{HTTP_HOST} ^([^.]+)\.([^.]+)
                RewriteCond %{REQUEST_FILENAME} !-f
                RewriteCond %{REQUEST_FILENAME} !-d
                RewriteRule ^(.*)$ /%1.%2/$1 [L]
        #end domain.tld


</VirtualHost>

Code (markup):

My issue comes with the www[DOT]domain[DOT]tld section... it worked perfectly on windows, but on Linux it always redirects to / (which is off limits for obvious reasons).

Help?