Description:
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I have PHP identically configured for two Web Sites under a single instance of IIS 6 on Windows Server 2003. In one, which has the identifier of 1 and runs on port 80, requests to .php files return normally. In the other, which has the identifier of 136095314 and listens on port 81, requests to PHP error for both ISAPI and CGI, with these messages:

When using php5isapi.dll: "No input file specified."
When using php-cgi.exe: CGI Error. The specified CGI application misbehaved by not returning a complete set of HTTP headers.

The two Web Sites have different document roots. This does seem important, as setting them to have the same document root fixes the issue.
Primary: c:\inetpub\wwwroot
Secondary: c:\inetpub\sandbox

I discovered this bug by first attempting to install PHP 5.0.3 on the secondary site. This bug is not dependent on the value of the doc_root variable in php.ini. It can be set correctly, set incorrectly, or unset. Other bugs suggest fixing doc_root to resolve this error, but I am certain that the value of the doc_root variable does not impact the error. Eventually I had no options left but to try PHP 5 on the primary site, which worked.

Web Service Extensions have been set up to permit both php5isapi.dll and php-cgi.exe, and the wildcard extension has been Allowed (to be sure this was not a simple security issue).

In both Web Sites, the PHP configuration under Home Directory -> Configuration -> Mappings is
Extension: .php
Executable: C:\php-5.0.3-Win32\php-cgi.exe %s or C:\php-5.0.3-Win32\php5isapi.dll
Verbs: All
Script Engine: Checked
Verify File Exists: Checked

Cache ISAPI Extensions is disabled. I frequently restarted the IIS Admin service is testing this.

For curious users, I was able to run PHP 5 without impacting PHP 4 with the instructions attached to this bug: http://bugs.php.net/bug.php?id=28448. This allows you to keep separate php.ini files.

Reproduce code:
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<?php

phpinfo();

?>

Expected result:
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Standard PHP info dump.

Actual result:
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"No input file specified.", or, when using php-cgi.exe: CGI Error. The specified CGI application misbehaved by not returning a complete set of HTTP headers.