We tried to install PHP 4 ISAPI Module on IIS 6 on a Windows Server 2003 SP2 at the office.
The only way we found out to make these extensions work, is by putting the extensions DLLs in the System32\inetsrv in the Windows directory. We did the same previously with the
php4isapi.dll and php4ts.dll to make PHP work. The system was asking for a password previously.
We cannot explain it, it seems like a problem only occuring with SP2 installed because we never had this problem before. Giving the right permission to the PHP and extensions folders didn't do anything good. It always gave use a permission denied error. We even tried to give full control to Everyone on the PHP folder, same result.
I hope it can help.