The primary reason is related to "clean urls".  It looks like your pages don't work with clean urls in IIS.  
 
More info can be found in the advanced install directory.  If you disable clean URLS, your site might work, but hte urls will not look as nice.   Use the IIS path to disable clean URLs and run the test again to see if their supported on your installation.
 
More info on Clean URL's and IIS can be found at:
 
http://drupal.org/node/3854
 
Dave

From: support-bounces@drupal.org [mailto:support-bounces@drupal.org] On Behalf Of Néstor
Sent: Tuesday, September 15, 2009 8:19 AM
To: support@drupal.org
Subject: [support] Drupal IIS (error 404) / Drupal Apache works

Hi people,

I have an interesting situation.  I have my web root directory
in D:\Inetpub\wwwroot\root

I have set up IIS on port 80 and Apache on Port:8999 and they both access
the same web root ( both servers access the same web pages ).

My Drupal-6.12 site is D:\Inetpub\wwwroot\root\nestor\scroller612\
I can access hte main page on both port 80 and port 8999
http://milhouse2/nestor/scroller612/
http://milhouse2:8999/nestor/scroller612/

Here is the problem, NONE of my links work past the main page on IIS
but they work on Apache.

What am I missing in IIS that makes my drupal site not work
except for the main page?

Example Apache port 8999 works:
http://milhouse2:8999/nestor/scroller612/as_dept/is/is_home

IIS port 80 does not work, gives error 404:
http://milhouse2/nestor/scroller612/as_dept/is/is_home

My phpinfo.php page shows mysql and php as:
PHP Version 5.2.9-2
MySQL Client API version        5.0.51a
Windows 2003
Drupal-6.12



Néstor