Multisite IIS 6 Ionics Isapi Rewrite Filter

Hi all

My set up is complicated but in summary is:

Win 2003 > IIS 6 > .NET site running on primary domain > WordPress in root of this domain running under Phalanger within the .NET application pool ??

Working URLS:
https://www.mysite.com/index.php
https://www.mysite.com/wp-admin/
https://www.mysite.com/anotherSite/index.php
https://www.mysite.com/anotherSite/wp-admin/

Not Working:
https://www.mysite.com/postname/
https://www.mysite.com/categoryname/postname/
https://www.mysite.com/anotherSite/
https://www.mysite.com/anotherSite/categoryname/postname/

My Isapi Rewrite File (iirf.ini) is below:

RewriteBase /
RewriteRule ^index\.php$ - [L]
#store original URL in custom header (substitute for missing REQUEST_URI header in IIS)
RewriteHeader X-REWRITE-URL:  ^$    %{REQUEST_URI}
# uploaded files
RewriteRule ^([_0-9a-zA-Z-]+/)?files/(.+) wp-includes/ms-files.php?file=$2 [L]
# add a trailing slash to /wp-admin
RewriteCond %{REQUEST_URI} ^.*/wp-admin$RedirectRule ^(.+)$ $1/ [R=301]
RedirectRule ^/index\.php/(.*)$ /$1 [I,R=301]
RewriteRule ^/(?!index\.php|wp-|xmlrpc)(.*)$ /index.php/$1 [I,L]
RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule . - [L]
RewriteRule  ^([_0-9a-zA-Z-]+/)?(wp-(content|admin|includes).*) $2 [L]
RewriteRule  ^([_0-9a-zA-Z-]+/)?(.*\.php)$ $2 [L,U]

Can anyone see the obvious issue? I will be eternally grateful if I can resolve this!

NOTE: I know the above sounds like a crazy set up but it’s the only way I could think to get multi site working within the root of the primary domain whilst keeping lots of legacy asp, aspx and html running whilst we slowly replace these!